Comskip problems with QAM recordings (HVR-1800)

[cyberfreak]

I'm using comskip with sagetv and it works fine for SD recordings but if I capture a show in QAM (which outputs as an MPG the same way the SD shows do) I get tons of these errors:

MP3 Audio or other unknown input, cannot decode
Audio PTS jumped 6 frames at frame 37, repairing timeline

MP3 Audio or other unknown input, cannot decode
Audio PTS jumped 4 frames at frame 44, repairing timeline

MP3 Audio or other unknown input, cannot decode
Audio PTS jumped 2 frames at frame 52, repairing timeline

MP3 Audio or other unknown input, cannot decode
Audio PTS jumped 2 frames at frame 55, repairing timeline

Then when comclean runs it complainns the audio is corrupt.

I have the audio set to ac3 in sage, and the properties of the file also say the audio is in ac3.

Has anyone seen this? Is it just that comskip wont work on QAM captures?