A number of people have had problems using Quicktime to create video that works with IBA. I'd recommend to use iMovie and export to iPad format. The videos generated that way work.
Interesting. I used iMovie and selected "File -> Export", selecting iPad as the target, without any problems. There are people here who reported that old codecs can interfere with Quicktime export and cause problems with videos for IBA.
See. That might help.