Random Render Line Glitch in AE CS6

Hey Adobe Community!
Although I have been quite happy with After Effects CS6, I have been running into some render glitches which are giving me real problems (whether CS6 is the culprit or not I don't know). On a number of jobs I am currently working on, the renders out of AE have strange bars that appear for about one frame at random times throughout the rendered clip. I can't find any pattern to the timecode or the screen location when they appear. Take a look below at the two pictures below for examples.
Quick note: This problem appears to be similar in some respects to the issue in this discussion (http://forums.adobe.com/message/4409423#4409423). Just thought I would post it for reference.
#1
#2
Here is some information about the two clips.
Clip for picture #1
Time: 2:06 (two seconds and six frames)
Output: Quicktime
Compression: None
Composition: There is 1 mask and some motion tracking
Clip for picture #2
Time: 20:06
Output: Quicktime
Compression: None
Composition: Utilizing the "Warp Stabilizer" in order to smooth camera movement.
This is obviously a problem that cannot continue since AE is a huge part of my work. I really appreciate any insight you can provide on this problem.
I know I have probably left out information that you would like, so if there are any questions please feel free to ask.
Thanks!
-Barrett

Premiere and AE should be able to handle H.264 clips directly out of the 5D and 7D without transcoding, but if you're still working with the original aquisition codec after switching to another program in the pipeline then that might be the problem. In that case, you might be forced to transcode your entire Premiere project to another lossless production codec using AME, which will give you the same quality as any other lossless codec. This is actually a step that a lot of editors take before doing anything with their footage, if they know it's going to go through several programs down the line. And if I understand correctly, Uncompressed QTs and high quality PNG QTs are both actually compressed. However, they are compressed with lossless formats. As Szalam said the QT PNG codec is the same quality as an Uncompressed QT, although I'd also suggest Apple ProRes 422 (HQ) if you have it. Uncompressed 10 bit, Uncompressed 8 bit and Animation are lossless, but the file sizes will be huge. If you have Black Magic you could also try that.

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