[popcornmix]

I will try, but I do no know where the EDL file is, or what to do with it when I find it. If you can tell me, I would appreciate it. If not, I will try to figure it out by myself.

Afraid I don't know anymore than you. I don't use mythtv (or any pvr backend). I'm aware that the code looks for a file named like the video file but with an edl extension.
This appears to define skip start and stop points which are used for automatically seeking past commercials.

If you work out how far out the skip is? (e.g. perhaps you lose the first 5 seconds of program before the commercial break, but it starts correctly after the break)
it might give some clues. e.g. there is a buffer of video+audio between the ARM and GPU that is typically a few seconds, and using the time from the wrong end of that buffer may explain a few seconds error.
If it's 30 seconds then it must be something else.