Suggesting something new to try or buy might not be what you're looking for, but I have been using TMPGEnc Xpress 4.0 to re-encode Divx files for playback on my Zune. The results are very good and output is very customizable. You can also queue-up a bunch of jobs and have them run all at once while you're away.

The program seems to natively support H.264 input and output. I will download and process your sample MOV file on my home computer and let you know how it turns out.