CS5.5 Rendering everything blue when queued from Prem Pro

My project is a custom 800x600 / 29.97 canvas using Quicktime Animation as the codec. Export> Media from Premiere Pro CS5.5. Using "Match Sequence Settings".
If I Export from Premiere Pro, it renders fine. But if I Queue the project into Adobe Media Encoder CS5.5, everything is rendered blue. And I mean really blue! Any guesses what is going on?

Hi everyone.
Okay, some news from me:
The problem also occurs exporting directly from Premiere Pro with a certain clip in the timeline
The problematic Clip is QT MOV 1920 x 1080 25P H.264
Applying Crop to this clip solves the problem
Using AME the problem occurs all over the timeline, but not at full certain clips, it occurs somewhere within the range of some clips
All Clips are QT MOV 1920 x 1080 25P PNG (except the one mentioned before that makes the problem even directly from Premiere Pro, this is H.264)
I have no special hardware, doing everything software even without NVidia-GPU
Exporting from 2 different machines give same (wrong) results.
MPEG I-Frame-only-Preview renders fine!
Everything is up to date according to the Adobe-Updater...
This is still extremely annoying, because QT provides the only reliable multi-compatible container with that much codecs available - especially the lossless well-compressing PNG-codec. For me this is an evil gap in workflow, QT PNG is my "allways and everywhere"-transport-codec!
By the way, is Premiere Pro capable of doing command-line rendering like AE? This way I could use Backburner to render from Premiere directly without using AME. I think it has to be capable of this, I suspect that AME does it this way. So if it is, can anyone tell me where to find the documentation for this? I didn´t find in in PrPro-help.
Thank you.
Sascha

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