Multi Camera in CS5.5 What is wrong?

For years I have been making usually two multi camera edits for dance recitals. I usually export the edited files
in the same format to another HD on my computer. 
I then go to that new directory and start a new project with the edited files.  Import the files into the new project
and line them up on the timeline. 
This year I have some files that have stuck with only Camera Two edits or sometimes Camera Two sound.  If I go back
to the original edit and make another file with the same timeline and a different name it works.  My only hunch is that
it has something to do with Indexing and Conforming when I start the new project with the edited files. 
Any suggestions?

My workflow is:
1. Import all footage (HDV)
2. Place all footage on timeline, syncing both cameras (this is for an entire show, 2 hours average duration) If I have any dropouts I find them where the audio of both tracks do not line up, so I make adjustments to the track that has the dropout and re-sync from that point on. If your second/alternative shot will not cover the dropout of the other camera, re import just the dropout section.
3. Nest into new sequence and do multicam edit
4. Close multicam and go back into the nested sequence and perform the fine edits, add titles and credits, cut out dead space, etc...
5. Export that sequence for DVD/Blu-Ray production.
For audio, I usually copy the audio from the first sequence (original) and paste it to the nested sequence after the multicam edit. Then I can choose which track of audio to use as I go, or make adjustments, etc...
I've never had any issues with cuts not holding, or audio being incorrect, with this workflow.

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