The save and load routines are something of a hack, so it's entirely possibly they're screwy. If I don't post back in a few days, remind me again. I need to get some time to sit down and fire up the code. Are all your autosaves the same way?
It's especially difficult to figure out with a zerobot sim because their genomes are supposed to be, well, random, so it's hard to pinpoint what exactly went wrong if anything.
What probably happened to your display, BTW, is something of an elusive graphics bug. You can fix it by locking/unlocking your display area (the little lock icon in the toolbar) and zooming in and out.