If there is a stutter in the film viewer, then FRAPS will show it as a stutter in its recorded information, whereas you will never, ever see a stutter from a film viewer export to AVI.
We get complaints about FRAPS and stutters all the time. FRAPS cannot synchronize with the game graphic engine, whereas the film viewer can.
The only problem with the export is the size of the film. Larger films tend to be more problematic. We have that on our bug list. Most of the problems have to do with the CODEC being used. There is a short list of ones that work.