Angela,
Your workflow should be along these lines, export via QuickTime (not QT conversion)self-contained using your sequence settings. Put this in Compressor and select 90 min. Best quality. Then put the m2v and audio file in DVDSP.
If you are not following these steps, this could explain your problem.
BTW, just to make sure, open up your exported movie in QT and see how the transitions look. If they’re okay, continue, otherwise, you may have some conflict going on in FCP or your plugins.
Have a wonderful day.