The only suspect here is QuirkyTime as QuickTime is often called.
Is there a diffrent workflow besides mdeia encoder (which I love)
maybe if I took the file into soundbooth and reexported it?
This became a major problem on my last job.
Not sure of the format limitations on Mac's but you might do similar to what one does with Export for/Import to Adobe Encore (if no "linking" is used). This entails Exporting as elemental streams, i.e. a Vdieo-only file and an Audio-only file - non-muxed. These two files are then Imported (Encore in this case) and "assembled" within the program. For the above, I use DV-AVI Type II (non-muxed) and PCM/WAV, or AC3 (non-muxed). This is for SD source/output. Obviously, with the Mac, further consideration will be needed. HD material will change my described workflow too, as regards to Export file format for the Video.