Couple of quick suggestions based on the info you provided.
- try rendering the timeline in Premiere Pro before outputting just to see if that helps
- clean your media cache and force all renders
- try a different version of quicktime
Thanks for your advice. I've deleted the cache files, rendered everything in the work area and exported a couple of versions. The problem isn't resolved, but at least we have some more information to troubleshoot.
The timeline is built at 1024x768 30fps (primary output is digital projector). If I export the clip at 1280x720 the blue doesn't crop up. When I export at native size 1024x768, or half resolution 512x384, the blue appears.
Opening it in QuickTime 7 doesn't help any. I can see the blue clip in QTX, QT7, AME's preview window and in a H.264 version exported from Sorenson Squeeze 6.5.
In PPCS4, I had a similar problem with certain clips if Maximum Render Quality was checked. It doesn't seem to have a bearing on this clip as I get the blue shift with and without Maximum Render Quality Checked.
What's really puzzling to me is that the four transition segments (three of which render correctly) are generated from the same AE comp. I simply turn on and off the necessary layers and render the segment I need. If it was a problem with the AE comp or project, I would think the problem would occur consistently between all four clips.
Lastly, the clip previews correctly in the PP timeline.
What do you suggest as a next step? In the meantime, I'm going to try and replace the affected clip with a direct link to the AE comp and see if that helps.
Are you making your sequence settings conform to the media? Easy way to do that is right click on media in CS5.5 and select 'create sequence from media'
The majority of the content for this project is still images. The only motion footage is the AE clips. I've tried replacing the AE comp with Dynamic link worked for the one I tried. I've also tried rendering it as DNXHD, which also turned blue, though Cineform did not.
The AE comps are set up at the project size, framerate, etc.