Are you exporting as quicktime conversion or quicktime movie? QT movie, self contained current settings is likely to be more stable that direct to Compressor or via QT conversion.
As mentioned, I tried two exports, Compressor to m2v file as well as QT self contained – both had the same glitches
Another thought is to copy paste the entire sequence into a new timeline if it is a corrupt sequence.
I copy and pasted the contents of the sequence into a new sequence and it did the same thing
Any large stills? It might be a corrupt file or even corruption in the sequence. It might play OK in the timeline because it is playing a render file.
I am not sure this is the problem, but it would be great if the solution could be found by discovering that it is.
How do I copy the clips in the sequence and make sure to break any connection with any existing render files?