combining Sequences - out of sync isssues

I am having a odd problem.

I have 40 sequences that I am putting together to make one large sequence. (20 dance numbers as separate sequences with 20 intros - one for each dance)

I am trying to add a transition between each sequence. Once I render the transistion, it makes the 2nd clip/sequence out of sync with the audio -- the incoming video clip starts to play then flashes and repeats itself -- the audio stays the same, so the video is then out of sync.

Now, if I "mess up" the render by moving the incoming clip and then putting it back and re-rendering, then it's fine. BUT, when I go to render other parts, it also re-renders the previous transitions that I've fixed (even though it shows it doesn't need to be rendered) and it messes it up again!

Are you following this? Does anyone understand what is happening or have any suggestions on what I can do to fix the issue???