The best way to describe what I've managed to get to work is what a friend suggested: 'that's some weird voodoo shit.' I over-installed the latest version (without uninstalling it) with the following version: 0.6.9 (SVN r3447), using MPlayer SVN r30369. The reason I think this is weird is that I'm pretty sure that version had substantial issues with audio track displacement. However, right now it's rendering even my most obnoxious h264 acceptably.
I don't understand at all what's changed, but while it works I think I'll leave it be and go with the voodoo explanation.
I have also deselected the draw in slices option, as suggested, and will watch a few movies without, then with it selected to consider whether it makes a major difference. Right now I can't really tell.
Thanks, redxii, for your help. BTW, during my fiddling around, I tried out VLC that seems to get a lot of mentions, but I thought it was an awful program. As was the Divx player (commercial software). SMPlayer and my av collection are gonna be friends for some time to come yet.