CS6 has problems with Cannon .mxf files that CS5 plays fine

On CS6 there are occational visual glitches that resembles DV drop out. A 1 hr spanned clip has audio going out of synch, audio length not matching video lenth.
Camera: Cannon XF100
Footage : 720p 60fps 35mbs
system Windows 7 Pro
premiere CS6.01
Core I7 930
16 GB ram
sysem drive: 128GB SSD
2 X 1TB media drives
GTX560
The same clips copied from the same flash card to a CS5 system plays without visual or audio glitches.
Core I7960
CS5.03
12GB ram
1tb media drive
gtx480
Any clue to why CS6 is having issues with the same footage CS5 is working beautifully with?

I also use the XF100 and have just about the same system setup as you (24GB RAM, Core i7 2600).  I have not observed any video glitches, but it doesn't mean I don't have them.  I just finished my first big shoot using two XF100's and I'm going to edit in CS6, so you have me a little concerned.
Could you describe the issue more?  Does it happen at the clip breaks?  How can you tell the audio doesn't match video length?  Are they different lengths on the timeline?  It could be that it's the conformed audio file.
How are you pulling in the video?  I've found that if I allow CS6 to interpet the spanned video as a single clip, it will conform the audio and it takes forever.  I have found it much more productive to just copy the individual MXF files to my system, and only the MXF files.  Then import them as assets and PPr will not conform the audio, it will just create PEK files for the audio waveforms.  I then select all the separate ~2GB clips and drag them to the timeline and they play fine.  For the multicam, I'll just bring in the first MXF file from each camera, sync them by timecode, then bring in the rest of camera "A" and the rest of camera "B".  Again, I haven't observed any issues, but it doesn't mean there aren't any.

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