Try to avoid using QT files as your imported source. Imported video is dependant on your timeline and Flash during recompression didn't convert it properly, that's probably your last frames are cut.

Solution for that will be either unencode your QT to uncompress state or use source video file (most likely AVI uncompressed).

Also I will suggest to work with external FLVs instead of creating video SWFs. It'll save you a lot of CPU processing