If you include source we might be able to help you more, but this is a method with which I have had success in writing many audio and video tracks to a quicktime movie – I use a single AVMutableComposition with AVMutableVideoComposition and AVAudioMix. I then write it like so:
AVAssetExportSession *session = [[[AVAssetExportSession alloc] initWithAsset:[project.composition copy] presetName:presetName] retain];
session.outputFileType = [session.supportedFileTypes objectAtIndex:0];
session.outputURL = [NSURL fileURLWithPath:[VeporterAppDelegate createMoviePath]];
session.videoComposition = project.videoComposition;
session.audioMix = project.audioMix;
session.metadata = project.metadata;
[session exportAsynchronouslyWithCompletionHandler:^{}];