I had a lot of trouble with HDV from a JVC camera. I would lose 7 seconds or so at every point where the camera was shut off. I think it has something to do with the way JVC terminates the data stream.
I also experiences problems such as yours, which I attributed to dropout on the tape.
My computer is also not that fast, so I beleive that may contribute.
I finally accepted that I would lose seconds around the camera shot end point, so I had the crew give adequate pre and post roll around the shot. Sorry I don’t have a better suggestion, but the HDV stream seems problematic. I have heard that Sony causes fewer problems, but you seem to have the same problems with either setup.