Here's an update.
I'm also using 3.1.2.6 and I'm having the same issue when I use the following settings:
High Quality (2-pass), Fixed Bitrate 1500, 30fps, Audio 64, Volume 100%, 640x352.

BUT, it works fine when I change my settings to the following:
Fast encoding (1-pass), Fixed Bitrate 1200, 29.97fps, Audio 128, Volume 300%, 640x352.

Go figure?? Tonight I'm going to experiment more with those settings to fine tune my backups, namely, I would rather use the 2-pass and 1500 fixed bitrate.

dj