Well the only fix I can use at the moment is to import the offending clips into Avid Media Composer (which I don't like using but will have to learn now) and then export to QT or wav, and re-import to Premiere.
Pretty disappointing. No reponse in nearly a year. I have a couple of corporate clients that are looking to make the switch from FCP. Because of my experience with DSLR in CS5.5 I had hoped to convince them to switch to CS 5.5. But they are xdcam inhouse and there is no way I could recommend CS 5.5 at this point. But 5 and 5.5 were quite an improvement. It is issues like this that will kill Premiere with the professional market. This is the nail in the coffin for Premiere, I think.