I am encoding my trailer using using Bitvice. The mov file - fully contained - is 2:16 mins. The Bitvice log file and the visual preview shows it encoding all the video. However, it is only written out partially.
I played around with bitrates and I get somewhere between 01:30 to 02:00 mins written out.
Wasted hours on this already! I am using Mountain Lion 10.8.4