If your issue is what I’m thinking of, then I’d like to share that we have come across the same problem. I have a few questions, though.
When you export, are you exporting in progressive frames or interlaced? It’s funny, you aren’t the only person who has come across this issue. The few other colleagues in this field we have discussed this with, have lended little to no help.
Also, just fyi, compressing to Windows Media will give you much smaller file sizes [still keeping good, relative quality] rather than using Quicktime compression schemes. The H.264 codec is great, but .WMV files work better with powerpoint presentations and other situations of that sort.
KennethGreen.net
Redefining Fine Art to Fine Wine.