I have been successfully capturing tv programs with an Elgato Video Capture device which produces 640x480 MP4 files.
I have been able to open these in MPEG Streamclip and save sections of them with no reencoding. The files play back with perfect audio sync as long as I remember to press Apple K (on my mac mini) to take me to the nearest keyframe before pressing I for the in point and O for the out point.

The problem is that I have upgraded to the Haupage PVR HD recorder which produces higher resolution MTS2 files which the software can automatically 'repackage' as MP4 files.

If I open these MP4 files in MPEG Streamclip and play them the audio is in sync. However, as soon as I start doing any editing the audio drifts out of sync. I had a 90 minute program from which I removed the adverts by making selections using Apple (CMD) K, I and O then cutting (X). By the end the audio was about 10 seconds out of sync.

Any ideas?