So, I now have an hour to kill while XXClone copies my hard drive to a spare hard drive...
Ellipsoid - cuboid collision is hard. I spent 2 days at work getting that working, because we figured it should be pretty easy to do, "after all, you can just transform everything into ellipsoid space and then you're doing cuboid - unit sphere tests". Well, it sounds easy, but it really isn't. You have a skewed cube, which you can't just plane test against the unit sphere because there's cases where that will give a false positive (When a corner of a cuboid is close to the ellipsoid).
Anyway, I got it working at last, with the help of some PDF I found on the Internet. Now I just need to get hemiellipsoid - cuboid collision working...
In other news, there is no other news. Fun.