Strange exporting problems from QT Pro

I have an odd problem that I hope someone can help me out with. Me and my partner run a video business. I do most of the editing and he does most of the graphics work. For 2 years now, we've had no problems exchanging and using each others files. He usually sends me QT files exported from either Adobe Premiere or After Effects. I also get a lot of photoshop files from him too. I usually import these files into my Avid, edit with them and export a final video. Never had a problem with any of his files before.
However, recently, when I use some of the photoshop files he sends me, after I edit with them and export a movie with mpeg-4 compression (from my Avid which uses QT components) I get black boxes all over the export, but only in the segments that use his new photoshop files. The rest of the export looks fine. He also recently gave me some edited video exported from his Premiere that I was going to convert using QT Pro. However when I convert to mpeg-4, I get the same black boxes. This time the source file he gave me was a video file, not a photoshop file but it was edited using a lot of Photoshop elements that he had created and edited with on his own system.
I have recently downloaded some updates including QT 7.6. So I thought that might have been the problem. But I just regressed back to 7.5.5 and the problem still exists. When I export my own footage or when I export old footage I have from him, everything is fine. But on certain new elements he gives me, I can not export to mpeg-4s. His source files look fine when I open them and play them and work in the Avid but once I export to mpeg-4 I get these issues.
Anyone have any idea why some elements that I am getting from him won't export correctly on my system? What may have changed that could cause this? This is kind of a big issue because we create a lot of content for mobile devices including Blackberries which prefer mpeg-4 video. So I need to figure this out. My partner hasn't changed or updated any software recently but there is some compatibility issue going on here.

I'm having the same issue as the original poster. I'm running the latest s/w (7.1.2) and I have removed all /Library/Quicktime items to the DT. I'm trying to export a .mpg file to Quicktime format.
The .mpg format is only playback supported by QT so it is usually best to use a third party MPEG based application like MPEG Streamclip (free) or ffmpegX (free) here if you wish to reatain audio content. If you still have a problem/are receiving an error message, then the problem could be with the file itself. Owing to its popularity, non-standard nature, and timecode sensitivity, such files are frequently corrupt -- especially when downloaded from peer-to-peer sources.

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