[netmask]

Could you post a MediaInfo file report on your video file. (text mode and then you can copy and paste the results)
I use ProjectX to remove commercials from my on air recordings.
Video is MPEG2 and Audio either AC3 or mpeg
Subtitles

I use demux mode as it fixes up a lot of transmission errors in this mode and edit via the arrow button in ProjectX - almost frame accurate. Make sure you click on the Cut Control tab bottom left to see the picture and the edit navigation tools.