From my experience, frequently when compressing Main Movie only, you end up with "the stutter." Good news is that simply unchecking the "Lightning Recode" option box always does the trick, at least for me. And I find the increase in compression time not using "Lightning Recode" is approximately 20% longer - so when you're dealing in hours anyway, who cares.
I've also observed that if the Main Movie compression projected time seems to be too short for the percentage compression number, then you'll end up with a stuttering backup copy. This is a qualitative judgement, meaning that if you've done enough backups of the main movie using compression, you generally get a feel for how long a compression time a given compression number requires. If the projected time looks to short to me after about 5 minutes, I usually bail and retry the backup with with "Lightning Recode" off.
Hopes this helps.
