If you are using an NTSC camara to capture PAL footage I think that you can get in this kind of problems. NTSc camaras can play PAL, and PAL camaras can play NTSC but what you are getting is not an standar video signal at all.
I would try to capture the PAL footage with a PAL camara, and if the sync issues remain with the audio back-up, export the audio back-up as an .aiff (or other PCM) and get rid of the TC in the audio file. Them sybc the PAL clip with the .aiff
Cheers,
Rafael