Premiere Pro CC MXF problems

Hi there,
I'm currently working on Premiere Pro CC. We've imported all of our clips from our C300 from a hard drive that was shipped to us. The folder structure in intact and the clips have been working fine, up until now.
I opened up my project today and I noticed a few clips were offline, they won't relink but instead give me a "generic error" message. The weird part is that there can be 2 clips from the same folder/file structure and one will work and one won't. Even weirder, we back up all of our media to two different folders. The folder we keep our working media on is getting thrown offline, the folder we archive everything... imports fine.
We also noticed that, even though we imported from the Media Browser, the .mxf extension appears. This hasn't been the case in any of our other projects. It's a recent addition. Not sure if that's part of the problem but it's weirdly timed to our offline problem. It looks like we dragged our footage from the finder but we did not.
Any ideas as to what's going on? One thought we had was that we recently upgraded to premiere 2014 but due to conversion issues and generally bugs, we decided to downgrade back to CC temporarily. We've completely uninstalled the 2014 suite and trashed all preferences.
C

Hi Matt,
I know that some other customers have complained about the quality of exports, as well. I have heard that 2 pass VBR might give bad quality. Can you try an encode with 1 Pass VBR instead? The quality should be just fine with 1 Pass VBR.
Thanks,
Kevin

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