MCEBuddy corrupts file

I’m having a problem with MCEbuddy 2.x in that once I run a file through MCEBuddy it corrupts the file.
To clarify this more in depth i’ll explain the exact steps.

Software used:
MCEbuddy 2.x (latest beta version) 2.4 beta 10
Donner version of comskip (however, using comskip or not has no bearing on the issue)
Videoredo TVSuite 5
Plex Server DVR (latest version)

Scenario #1
Plex DVR creates a .ts file
MCEBuddy grabs this file via script, runs comskip, converts to .mp4, .mkv whatever.
File plays just fine no problem.
If minor editing is required I use Videoredo to cut missed commercials and clean the video up.
Save the file and the audio stream is damaged.

Scenairo #2
Plex DVR creates a .ts file
Do NOT run the file through MCEBuddy
open the .ts file in Videoredo, make cuts, save the file.
No audio or video issues.

So my problem is any file that is processed with MCEbuddy then edited with Videoredo the audio stream is damaged. Long sections of audio are missing or “squeeks” throughout the video.

I do not have any issues processing the .ts file directly in Videoredo and saving the output.

Any suggestions on how to resolve this issue would be greatly appreciated.

You can start by attaching the conversion log.
You can tweak the profile, change the encoder and see if that make a difference. Try disabling remuxing in the conversion task expert settings and see if that makes any difference.