Sorry Simon I never found an resolution, I have tried (snap on/off, etc.) I just pay super close attention to when I make a cut if there is some sync issues. For some reason as I make more and more cuts, One audio channel is off.
I use shit+click for razor tool now and it cuts all lines (audio+video)
Your issue sounds very different, the audio is out of sync when you import? Has it trans-coded everything yet? Or “index” I guess is the term. Sometimes, If I have left my Premiere CC open too long the video freezes in the preview window. Closing/opening the program helps me, not sure if that will help you. Best of luck!