Ohhhhhh. Okay, yeah, I get it now. "Using Quicktime Conversion" is one of those things Final Cut does, but doesn't seem to do well. It's notoriously unreliable.
Like Corbett said, your best workflow for getting out of Final Cut to a file format (as opposed to videotape) is to export a self-contained Quicktime movie, then do any post-processing you need to on that.