I have a years experience working with MC6, and have never come across this new issue importing.
I just installed MC6 and am trying to import some 5D footage, something I have done many times before with out a problem. For some reason this time, no matter what settings i change and whether I import or link to AMA, the clips come in with a flashing green screen and odd digital distortion as the clips play. I checked to see if it was a missing codec issue and that wasn't it. In my researching I found someone with a similar issue, and they were told to try copying the footage to the desktop and try importing. I did this and sure enough it worked, but that's not a solution. Id like to work from my external drives. Iv also tried copying to a different external and I get the same issue.
iMac OS x 10.8.3
processor 3.4 GHz Intel Core i7
Mem 16 gb 1333 MHz DDR3
Graphics AMD Radeon HD 6970 1 GB