[Paul Dougherty]"a mis-match. Which doesn't make sense, there is no other copy to that it could be mixed up with... corrupted?"
That's what it sounds like.
Check your source media directory for clips that might have a -v added to the filename or no .mov suffix, stuff like that. I'd be just as baffled if for some reason a file became "spanned" if there were some OS issues. Normally when this happens, I end up manually moving source clips and re-imbedding, &c.
"I always pass on free advice -- its never of any use to me" Oscar Wilde.