I can't even imagine any possible way for this to happen, outside of operator error like exporting the wrong sequence, or having the effect disabled.
Neither can I. Very weird. Even weirder, if I output just a small section of the video where the effect is applied, it would often output just fine, but do the whole 34 minute sequence and all bets are off.
I did notice this first started happening when I duplicated a sequence (so I could make changes and give myself a backup). It seems that the biggest issue are with copied files, but I have not tested enough to say for sure that is the issue or just coincidental.
I imagine that some of this may be why Adobe has not unlocked it in CS6-I used the hack to get it working, so I really cannot complain. But it is weird.
Ooooooh, Timewarp. My brain just filled in the wrong gaps and I thought you were using Time Remapping.
Well, given the effect isn't native to PP, it's not that surprising there may be issues.
I imagine that some of this may be why Adobe has not unlocked it in CS6-I used the hack to get it working.
The mentioned 'hack' to enable Time Warp Effect in CS6:
Ctrl+F12, Debug Database View, TimeWarpFilterEnabled > true.
Not Adobe endorsed, results may vary.