I have a quite similar problem, just from the start, when I bought the software. ALL my clips, taken with a Sanyo Xacti in full HD and H.264 are, after stabilizing with the excellent deshaker inside Video Pad (which was the very reason, I bought it!) out of sync.
Soundtrack starts after stabilizing with 2-3 sec delay, and also ends 2-3 sec before the end of the clip. I asked support, they only told me, to update the codecs, which I did, but with no success in the result.
Any ideas, what could solve the problem?
Thx, Axel