WTV Unprocessed creates video with "staggers" stop-motion effect

I have one channel in NZ called PRIME that seems to use a weird encoding, in as much as it doesn’t behave well in WMC to FF / 30sec / 8 sec skips. It usually over-skips, under-skips, or freezes for 30 seconds at a time.
VLC and WMP also have problems in playing this particular channel’s WTV files.

So I’d thought to remove the commercials using the WTV Unprocessed profile.
The resulting video has what I can only call a staggering or stop-motion effect.

The WTV unprocessed profile is only supposed to perform the commercial cut, and stitch the segments together. The other WTV profiles also create the same effect.
MediaInfo shows exactly the same details for the unprocessed video as it does for the processed video, with the exception of the file size.

I did modify the WTV Unprocessed profile to replace the ffmpeg with avidemux as mentioned in the conversion output log. Unfortunately, that didn’t help - I still get converted videos with the stop-motion effect.

I then processed the same file with the MP4 Normal profile.
This produced a nice watchable file, without the staggers, but unfortunately, WMC doesn’t recognise the resulting MP4 as a valid file in Recorded TV., and also loses the program description, etc.

So now I’m stuck … I’d like to nut out this perplexing case, and get a watchable file.
log file of one of the recent WTV Unprocessed

INFORMATION> --> Windows OS Version -> Microsoft Windows NT 6.1.7601 Service Pack 1 (WIN_7_2008_SERVER_R2, Professional)
INFORMATION> --> Windows Platform -> 64 Bit
INFORMATION> --> MCEBuddy Build Platform -> 64 Bit
INFORMATION> --> MCEBuddy Build Version : 2.4.8.1
INFORMATION> --> MCEBuddy Build Date : 01/24/2018 17:02:36
INFORMATION> --> MCEBuddy Running as Service : True
INFORMATION> 2018-08-24T08:29:58 MCEBuddy.Engine.ConversionJob --> Current System language is English (New Zealand) (eng)
INFORMATION> 2018-08-24T08:29:58 MCEBuddy.Engine.ConversionJob --> Converting file -> C:\Incoming_Vids\Prime Flicks- The Number 23_PRIME_2018_08_06_21_30_00.wtv
INFORMATION> 2018-08-24T08:30:06 MCEBuddy.Engine.ConversionJob --> Running custom commands
INFORMATION> 2018-08-24T08:30:06 MCEBuddy.Transcode.CustomCommand --> No custom commands found
INFORMATION> 2018-08-24T08:30:06 MCEBuddy.Engine.ConversionJob --> Getting show information and banner from Internet sources
INFORMATION> 2018-08-24T08:30:06 MCEBuddy.MetaData.VideoMetaData --> Extracting MCE Tags
INFORMATION> 2018-08-24T08:30:06 MCEBuddy.MetaData.VideoMetaData --> Skipping downloading Series details
INFORMATION> 2018-08-24T08:30:06 MCEBuddy.Engine.ConversionJob --> Running custom commands
INFORMATION> --> Skipping Renaming by Series details
INFORMATION> --> Skipping Renaming by Series details
INFORMATION> 2018-08-24T08:30:06 MCEBuddy.Transcode.CustomCommand --> No custom commands found
INFORMATION> 2018-08-24T08:30:06 MCEBuddy.Engine.ConversionJob --> Checking for disk space
INFORMATION> 2018-08-24T08:30:06 MCEBuddy.Engine.ConversionJob --> Checking for SRT File
INFORMATION> 2018-08-24T08:30:06 MCEBuddy.Engine.ConversionJob --> Checking for EDL, EDLP, VPRJ or DTB XML files
INFORMATION> --> Comskip version : DONATOR
INFORMATION> 2018-08-24T08:30:14 MCEBuddy.RemuxMediaCenter.RemuxMCERecording --> AllowH264CopyRemuxing will run fast for commercial detection, using donator version of Comskip
INFORMATION> 2018-08-24T08:30:14 MCEBuddy.Engine.ConversionJob --> Remuxing recording
INFORMATION> 2018-08-24T08:30:14 MCEBuddy.RemuxMediaCenter.RemuxMCERecording --> Fast Remuxing
INFORMATION> 2018-08-24T08:30:14 MCEBuddy.RemuxMediaCenter.RemuxMCERecording --> Copy remux loop 0
INFORMATION> 2018-08-24T08:33:39 MCEBuddy.Engine.ConversionJob --> Trimming video recording
INFORMATION> 2018-08-24T08:33:39 MCEBuddy.Engine.ConversionJob --> Analyzing video information
INFORMATION> 2018-08-24T08:33:39 MCEBuddy.VideoProperties.VideoInfo --> Reading MediaInfo from C:\Program Files\MCEBuddy2x\working0\Prime Flicks- The Number 23_PRIME_2018_08_06_21_30_00.ts
INFORMATION> 2018-08-24T08:33:45 MCEBuddy.VideoProperties.VideoInfo --> Supplementing Media information using FFMPEG
INFORMATION> 2018-08-24T08:33:47 MCEBuddy.VideoProperties.VideoInfo --> Reading Original File Media information
INFORMATION> 2018-08-24T08:33:53 MCEBuddy.VideoProperties.VideoInfo --> Skipping crop information
INFORMATION> 2018-08-24T08:33:56 MCEBuddy.Engine.ConversionJob --> Advertisement scan
INFORMATION> 2018-08-24T08:33:56 MCEBuddy.CommercialScan.Scanner --> Scanning commercials with Comskip
INFORMATION> 2018-08-24T08:33:58 MCEBuddy.AppWrapper.Comskip --> Process priority changed to Normal
INFORMATION> 2018-08-24T08:42:59 MCEBuddy.CommercialScan.Scanner --> Skipping EDLP, using EDL file for commercial removal
INFORMATION> 2018-08-24T08:43:00 MCEBuddy.Engine.ConversionJob --> Running custom commands
INFORMATION> --> Skipping Renaming by Series details
INFORMATION> --> Skipping Renaming by Series details
INFORMATION> 2018-08-24T08:43:00 MCEBuddy.Transcode.CustomCommand --> No custom commands found
INFORMATION> 2018-08-24T08:43:00 MCEBuddy.Engine.ConversionJob --> PRE-Removing commercials for Ext -> .wtv
INFORMATION> 2018-08-24T08:43:00 MCEBuddy.Engine.ConversionJob --> Checking if commercials were found
INFORMATION> 2018-08-24T08:43:00 MCEBuddy.Engine.ConversionJob --> Removing commercials
INFORMATION> 2018-08-24T08:43:00 MCEBuddy.CommercialScan.Remover --> Removing commercials using CutTS ext -> .ts
INFORMATION> 2018-08-24T08:43:00 MCEBuddy.CommercialScan.Remover --> CutTS: Cutting commercials from video - segment 0
INFORMATION> 2018-08-24T08:43:12 MCEBuddy.CommercialScan.Remover --> CutTS: Cutting commercials from video - segment 1
INFORMATION> 2018-08-24T08:43:20 MCEBuddy.CommercialScan.Remover --> CutTS: Cutting commercials from video - segment 2
INFORMATION> 2018-08-24T08:43:33 MCEBuddy.CommercialScan.Remover --> CutTS: Cutting commercials from video - segment 3
INFORMATION> 2018-08-24T08:43:47 MCEBuddy.CommercialScan.Remover --> CutTS: Cutting commercials from video - segment 4
INFORMATION> 2018-08-24T08:44:01 MCEBuddy.CommercialScan.Remover --> CutTS: Cutting commercials from video - segment 5
INFORMATION> 2018-08-24T08:44:13 MCEBuddy.CommercialScan.Remover --> CutTS: Cutting commercials from video - segment 6
INFORMATION> 2018-08-24T08:44:23 MCEBuddy.CommercialScan.Remover --> CutTS: Cutting commercials from video - segment 7
INFORMATION> 2018-08-24T08:44:36 MCEBuddy.CommercialScan.Remover --> CutTS: Cutting commercials from video - segment 8
INFORMATION> 2018-08-24T08:44:50 MCEBuddy.CommercialScan.Remover --> CutTS: Cutting commercials from video - segment 9
INFORMATION> 2018-08-24T08:45:02 MCEBuddy.CommercialScan.Remover --> CutTS: Merging commercial free segments into new video
WARNING> 2018-08-24T08:45:11 MCEBuddy.CommercialScan.Remover --> Using FFMPEG instead of AVIDemux to merge tracks. There may be artifacts/issues with the video at the merged segments, set CommercialMergeTool=avidemux in the profile if you are facing issues
INFORMATION> 2018-08-24T08:46:56 MCEBuddy.Engine.ConversionJob --> ReAnalyzing video information post commercial removal before video conversion
INFORMATION> 2018-08-24T08:46:56 MCEBuddy.Engine.ConversionJob --> Analyzing video information
INFORMATION> 2018-08-24T08:46:56 MCEBuddy.VideoProperties.VideoInfo --> Reading MediaInfo from C:\Program Files\MCEBuddy2x\working0\Prime Flicks- The Number 23_PRIME_2018_08_06_21_30_00.ts
INFORMATION> 2018-08-24T08:47:00 MCEBuddy.VideoProperties.VideoInfo --> Supplementing Media information using FFMPEG
INFORMATION> 2018-08-24T08:47:06 MCEBuddy.VideoProperties.VideoInfo --> Reading Original File Media information
INFORMATION> 2018-08-24T08:47:13 MCEBuddy.VideoProperties.VideoInfo --> Skipping crop information
INFORMATION> 2018-08-24T08:47:13 MCEBuddy.Engine.ConversionJob --> Analyzing video information
INFORMATION> 2018-08-24T08:47:13 MCEBuddy.VideoProperties.VideoInfo --> Reading MediaInfo from C:\Program Files\MCEBuddy2x\working0\Prime Flicks- The Number 23_PRIME_2018_08_06_21_30_00.ts
INFORMATION> 2018-08-24T08:47:15 MCEBuddy.VideoProperties.VideoInfo --> Supplementing Media information using FFMPEG
INFORMATION> 2018-08-24T08:47:18 MCEBuddy.VideoProperties.VideoInfo --> Reading Original File Media information
INFORMATION> 2018-08-24T08:47:20 MCEBuddy.VideoProperties.VideoInfo --> Skipping crop information
INFORMATION> 2018-08-24T08:47:20 MCEBuddy.Engine.ConversionJob --> Converting
INFORMATION> 2018-08-24T08:47:21 MCEBuddy.Transcode.Convert --> Using special case COPY for converter
INFORMATION> 2018-08-24T08:47:21 MCEBuddy.Transcode.ConvertWithCopy --> Checking for Unsupported profile for container / codec combination
INFORMATION> 2018-08-24T08:47:21 MCEBuddy.Transcode.Convert --> Converting with COPY
INFORMATION> 2018-08-24T08:47:21 MCEBuddy.Transcode.ConvertWithCopy --> Setting up General conversion parameters :
INFORMATION> 2018-08-24T08:47:21 MCEBuddy.Transcode.ConvertWithCopy --> Setting up input file name parameters
INFORMATION> 2018-08-24T08:47:21 MCEBuddy.Transcode.ConvertWithCopy --> Setting up video conversion parameters :
INFORMATION> 2018-08-24T08:47:21 MCEBuddy.Transcode.ConvertWithCopy --> Is preset video size -> False
INFORMATION> 2018-08-24T08:47:21 MCEBuddy.Transcode.ConvertWithCopy --> Setting up crop parameters
INFORMATION> 2018-08-24T08:47:21 MCEBuddy.Transcode.ConvertWithCopy --> Fixed resolution video, no resizing
INFORMATION> 2018-08-24T08:47:21 MCEBuddy.Transcode.ConvertWithCopy --> Setting up aspect ratio if required
INFORMATION> 2018-08-24T08:47:21 MCEBuddy.Transcode.ConvertWithCopy --> Setting up bitrate and quality parameters
INFORMATION> 2018-08-24T08:47:21 MCEBuddy.Transcode.ConvertWithCopy --> Setting up audio conversion parameters :
INFORMATION> 2018-08-24T08:47:21 MCEBuddy.Transcode.ConvertWithCopy --> Skipping over Audio Track selection, no language request or only one Audio Track found
INFORMATION> 2018-08-24T08:47:21 MCEBuddy.Transcode.ConvertWithCopy --> Setting up Audio channels
INFORMATION> 2018-08-24T08:47:21 MCEBuddy.Transcode.ConvertWithCopy --> Setting up Output filename
INFORMATION> 2018-08-24T08:47:21 MCEBuddy.Transcode.ConvertWithCopy --> Replacing user specified parameters
INFORMATION> 2018-08-24T08:47:21 MCEBuddy.Transcode.ConvertWithCopy --> Converting the video - Main conversion
INFORMATION> 2018-08-24T08:48:51 MCEBuddy.Transcode.ConvertWithCopy --> Correcting Audio Delay if required
INFORMATION> 2018-08-24T08:48:52 MCEBuddy.Transcode.ConvertWithCopy --> Remuxing video if required
INFORMATION> 2018-08-24T08:50:39 MCEBuddy.Transcode.RemuxExt --> FFMPEG ReMux moving file
INFORMATION> 2018-08-24T08:50:40 MCEBuddy.Engine.ConversionJob --> Converted File : C:\Program Files\MCEBuddy2x\working0\Prime Flicks- The Number 23_PRIME_2018_08_06_21_30_00.wtv
INFORMATION> 2018-08-24T08:50:40 MCEBuddy.Engine.ConversionJob --> Checking if commercials were found
INFORMATION> 2018-08-24T08:50:40 MCEBuddy.Engine.ConversionJob --> Commercials not found or cutting already completed
INFORMATION> 2018-08-24T08:50:40 MCEBuddy.Engine.ConversionJob --> Writing show information
INFORMATION> 2018-08-24T08:50:57 MCEBuddy.Engine.ConversionJob --> Renaming file using show information
INFORMATION> --> Skipping Renaming by Series details
INFORMATION> 2018-08-24T08:50:57 MCEBuddy.Engine.ConversionJob --> Running custom commands
INFORMATION> --> Skipping Renaming by Series details
INFORMATION> 2018-08-24T08:50:57 MCEBuddy.Transcode.CustomCommand --> No custom commands found
INFORMATION> 2018-08-24T08:50:57 MCEBuddy.Engine.ConversionJob --> Moving converted file to destination
INFORMATION> 2018-08-24T08:50:57 MCEBuddy.Engine.ConversionJob --> Moving converted file C:\Program Files\MCEBuddy2x\working0\Prime Flicks- The Number 23_PRIME_2018_08_06_21_30_00.wtv to C:\Temp_Vids\Prime Flicks- The Number 23_PRIME_2018_08_06_21_30_00.wtv
INFORMATION> 2018-08-24T08:50:57 MCEBuddy.Engine.ConversionJob --> Running custom commands
INFORMATION> --> Skipping Renaming by Series details
INFORMATION> 2018-08-24T08:50:57 MCEBuddy.Transcode.CustomCommand --> No custom commands found
INFORMATION> 2018-08-24T08:50:57 MCEBuddy.Engine.ConversionJob --> Success - All done!
INFORMATION> 2018-08-24T08:50:57 MCEBuddy.Engine.ConversionJob -->
INFORMATION> --> Total time taken by conversion (hh:mm:ss) -> 00:20:51

It’s better to set your logs to debug and “attach” the conversion log. Its’ more readable and has lots more information to analyze and see what’s going on.
You may also want to upload your original video and conversion log to the MCEBuddy upload server for us to analyze it