Exporting movies with Quicktime Pro

I have Quicktime Pro and have been trying to use it to merge some video clips I've taken myself. I'm not doing anything particularly fancy, but I tried to upload a Quicktime video file to my Bebo account.. the video consisted of two clips merged together, each with a different sound track. It played fine in Quicktime but when I'd uploaded it to Bebo, it played only the first few seconds with sound (the first clip I'd added to the file) and for the rest the sound was missing. Do I need to 'flatten' all the video/audio properties or something before it'll work? I know that the Bebo video uploader supports Quicktime movie files, and I don't want to use MPEG4 because it will mean a considerable loss in quality. Any advice appreciated. Thanks.