Subtitles out of sync - how to do this workaround?

I am recording from an HDHomeRun Prime with Cablecard using Windows Media Center. I am using the paid for comskip for commercial detection (seems to work just about spot on). However, the subtitle file is pretty much always out of sync. I have played with the subtitle offset settings many times, thought I got it right with a test file, but subsequent recordings are not correct. Its like the offset needs to be different for each recording.

So, my thought is to do the following:

  1. Identify commercial segments
  2. Convert full length video into MP4 while burning subtitles
  3. Cut MP4 commercials out

This should result in having the subtitles burned in before cutting the video, so they should not be out of sync ever. Thoughts? How would I set it up to make this happen?

Thanks.