I've been having some problems exporting directly to H.264 for quite some time now. Whenever I do, I end up with glitches such as the video flashing with a frame or two of green, footage out of sync and messed up and transitions that don't play.
I've experimented with rendering it all in my sequence as different codecs (Prores, MPEG 4, etc) And still, exporting to H.264 yields the same results.
I've trashed my preferences in hopes that was an easy cure, but the problem still persists. Could anybody offer some advice?