It's happened a couple more times now, I'll pull the logs tomorrow and post them.
So, mala focus logger did not resolve the problem. The logs state that "no window has focus" and then Focus Logger attempts to shift focus to Mala and fails. It doesn't give a detailed reason why it fails, but looking at the log history it seems pretty clear that nothing has focus.
I'm thinking at this point that perhaps Plugins may cause the problem? This problem has actually gotten worse the more plugins I've used. Before I used the autolauncher I never had the problem. After using the autolauncher plugin, I had it twice in the span of a month. Now, since adding in focus logger, I'm getting it about once every 2 days with reasonable consistency. I'm still not sure how to reproduce it reliably though, and it's always after exiting an emulator and losing focus.
Logs coming soon, but they don't appear to tell much other than it's a mystery

Edit: I found the exact line that was in adamc's log file... Malafocuslogger doesn't fix focus for me either, I'm using WinXPsp3.
No window has focus: setting focus to MaLa.
-- Failed to set focus to MaLa.
Again, I'll post the log tomorrow. The only out of the box thing I've done with Mala was use plugins, and it seems to get worse with more plugins. Now I'm curious, how does Mala handle plugins, is it attempting to reload them or something which can steal focus if timed properly? I'm still even using the default layout with a different background/wallpaper and this is a squeaky clean install of xp.