Upgraded MCEBuddy and now comericals aren't removing?

It appears to be an issue your custom comskip location or file permissions etc. I just did a test on the version you’re using and it’s working fine. This is what the logs look like when it’s accessible

→ Checking for donator version of Comskip
2019-03-18T16:30:24 MCEBuddy.AppWrapper.Comskip → Launching process D:\MCEBuddy\MCEBuddy2x\MCEBuddy.ServiceCMD\bin\x64\Debug\comskip\comskip.exe
2019-03-18T16:30:24 MCEBuddy.AppWrapper.Comskip → Process arguments -h
2019-03-18T16:30:32 MCEBuddy.AppWrapper.Comskip → Setting process priority to Normal
2019-03-18T16:30:32 MCEBuddy.AppWrapper.Comskip → The commandline used was:
2019-03-18T16:30:32 MCEBuddy.AppWrapper.Comskip → The commandline used was:
2019-03-18T16:30:32 MCEBuddy.AppWrapper.Comskip → Comskip 0.82.007, made using ffmpeg
2019-03-18T16:30:32 MCEBuddy.AppWrapper.Comskip → D:\MCEBuddy\MCEBuddy2x\MCEBuddy.ServiceCMD\bin\x64\Debug\comskip\comskip.exe -h
2019-03-18T16:30:32 MCEBuddy.AppWrapper.Comskip → D:\MCEBuddy\MCEBuddy2x\MCEBuddy.ServiceCMD\bin\x64\Debug\comskip\comskip.exe -h
2019-03-18T16:30:32 MCEBuddy.AppWrapper.Comskip → Donator build
2019-03-18T16:30:32 MCEBuddy.AppWrapper.Comskip → Usage:
2019-03-18T16:30:32 MCEBuddy.AppWrapper.Comskip → comskip [-h|–help] [-w|–debugwindow] [-n|–playnice] [–zpcut] [–zpchapter] [–scf] [–videoredo] [–videoredo3] [–csvout] [–quality] [–plist] [-m|–demux] [–hwassist] [–cuvid] [–vdpau] [–dxva2] [–decoders] [–threads=] [-p|–pid=] [-t|–ts] [-d|–detectmethod=] [-v|–verbose=] [-u|–dump=] [-s|–play] [–timing] [-q|–quiet] [–ini=] [–logo=] [–cut=] [–output=] [–output-filename=] [–selftest=] []
2019-03-18T16:30:32 MCEBuddy.AppWrapper.Comskip → -h, --help Display syntax
2019-03-18T16:30:32 MCEBuddy.AppWrapper.Comskip → -w, --debugwindow Show debug window
2019-03-18T16:30:32 MCEBuddy.AppWrapper.Comskip → -n, --playnice Slows detection down
2019-03-18T16:30:32 MCEBuddy.AppWrapper.Comskip → --zpcut Outputs a ZoomPlayer cutlist
2019-03-18T16:30:32 MCEBuddy.AppWrapper.Comskip → --zpchapter Outputs a ZoomPlayer chapter file
2019-03-18T16:30:32 MCEBuddy.AppWrapper.Comskip → --scf Outputs a simple chapter file for mkvmerge
2019-03-18T16:30:32 MCEBuddy.AppWrapper.Comskip → --videoredo Outputs a VideoRedo cutlist
2019-03-18T16:30:32 MCEBuddy.AppWrapper.Comskip → --videoredo3 Outputs a VideoRedo3 cutlist
2019-03-18T16:30:32 MCEBuddy.AppWrapper.Comskip → --csvout Outputs a csv of the frame array
2019-03-18T16:30:32 MCEBuddy.AppWrapper.Comskip → --quality Outputs a csv of false detection segments
2019-03-18T16:30:32 MCEBuddy.AppWrapper.Comskip → --plist Outputs a mac-style plist for addition to an EyeTV archive as the ‘markers’ property
2019-03-18T16:30:32 MCEBuddy.AppWrapper.Comskip → -m, --demux Demux the input into elementary streams
2019-03-18T16:30:32 MCEBuddy.AppWrapper.Comskip → --hwassist Activate Hardware Assisted video decoding
2019-03-18T16:30:32 MCEBuddy.AppWrapper.Comskip → --cuvid Use NVIDIA Video Decoder (CUVID), if available
2019-03-18T16:30:32 MCEBuddy.AppWrapper.Comskip → --vdpau Use NVIDIA Video Decode and Presentation API (VDPAU), if available
2019-03-18T16:30:32 MCEBuddy.AppWrapper.Comskip → --dxva2 Use DXVA2 Video Decode and Presentation API (DXVA2), if available
2019-03-18T16:30:32 MCEBuddy.AppWrapper.Comskip → --decoders List all decoders and exit
2019-03-18T16:30:32 MCEBuddy.AppWrapper.Comskip → --threads= The number of threads to use
2019-03-18T16:30:32 MCEBuddy.AppWrapper.Comskip → -p, --pid= The PID of the video in the TS
2019-03-18T16:30:32 MCEBuddy.AppWrapper.Comskip → -t, --ts The input file is a Transport Stream
2019-03-18T16:30:32 MCEBuddy.AppWrapper.Comskip → -d, --detectmethod= An integer sum of the detection methods to use
2019-03-18T16:30:32 MCEBuddy.AppWrapper.Comskip → -v, --verbose= Verbose level
2019-03-18T16:30:32 MCEBuddy.AppWrapper.Comskip → -u, --dump= Dump the cutscene at this frame number
2019-03-18T16:30:32 MCEBuddy.AppWrapper.Comskip → -s, --play Play the video
2019-03-18T16:30:32 MCEBuddy.AppWrapper.Comskip → --timing Dump the timing into a file
2019-03-18T16:30:32 MCEBuddy.AppWrapper.Comskip → -q, --quiet Not output logging to the console window
2019-03-18T16:30:32 MCEBuddy.AppWrapper.Comskip → --ini= Ini file to use
2019-03-18T16:30:32 MCEBuddy.AppWrapper.Comskip → --logo= Logo file to use
2019-03-18T16:30:32 MCEBuddy.AppWrapper.Comskip → --cut= CutScene file to use
2019-03-18T16:30:32 MCEBuddy.AppWrapper.Comskip → --output= Folder to use for all output files
2019-03-18T16:30:32 MCEBuddy.AppWrapper.Comskip → --output-filename= Filename base to use for all output files
2019-03-18T16:30:32 MCEBuddy.AppWrapper.Comskip → --selftest= Execute a selftest
2019-03-18T16:30:32 MCEBuddy.AppWrapper.Comskip → Input file
2019-03-18T16:30:32 MCEBuddy.AppWrapper.Comskip → Output folder for cutlist
2019-03-18T16:30:32 MCEBuddy.AppWrapper.Comskip → Detection Methods
2019-03-18T16:30:32 MCEBuddy.AppWrapper.Comskip → 1 - Black Frame
2019-03-18T16:30:32 MCEBuddy.AppWrapper.Comskip → 2 - Logo
2019-03-18T16:30:32 MCEBuddy.AppWrapper.Comskip → 4 - Scene Change
2019-03-18T16:30:32 MCEBuddy.AppWrapper.Comskip → 8 - Resolution Change
2019-03-18T16:30:32 MCEBuddy.AppWrapper.Comskip → 16 - Closed Captions
2019-03-18T16:30:32 MCEBuddy.AppWrapper.Comskip → 32 - Aspect Ratio
2019-03-18T16:30:32 MCEBuddy.AppWrapper.Comskip → 64 - Silence
2019-03-18T16:30:32 MCEBuddy.AppWrapper.Comskip → 128 - CutScenes
2019-03-18T16:30:32 MCEBuddy.AppWrapper.Comskip → 255 - USE ALL AVAILABLE
Process exited with code 2
INFORMATION> → Comskip version : DONATOR

Where as in your case it’s not even running and exiting with code 255. I think it’s a file permission issue with your comskip setup. Try using the built in version that ships with MCEBuddy and then move onto your custom version and check that the file is accessible to all users.