I want to put separate post here, because I know many people get to same problem.
HDV Capture in PPro, doesn't really do well (gets easily out of sync), so I suggest you use HDVSplit, as it does, it's job to capture, perfectly. It can separates files, according to scenes and mark then with date and time. PPro has no problems to import this files and work with them as source.
Same m2t source files can easily be encoded with, let say Dr. DivX to directly get compressed versions, but be careful to do editing with m2t files rather than compressed files.
The problem seems to stem from capturing over the places where stopped and restarted your camera. This breaks the group of 15 pictures (GOP) and Premiere Pro doesn't seem to be able to deal with broken GOPs well.