Eventually, I got the Orbiter to work with UI2. The only problem was that I couldn't turn on alpha blending even though DRI and composite was all working fine. Still, I was willing to live with this.
However, when I first installed the core it was using another monitor and when I connected the monitor it was going to use for good it recreated the xorg.conf and enabled transparency. I'm really not sure why it did this, but now the CPU usage for the X process gets progressively higher until it reaches around 100% (takes about 5 minutes) and makes the system useless. Note that it only does this when the Orbiter is drawing on the screen, otherwise the X process has normal CPU usage. I've tried disabling the composite extension in xorg.conf, but then then Orbiter get stuck in an endless loop saying that it couldn't enable transparency. I also tried changing the orbiter UI to not use transparency, but the admin site doesn't allow me to change those options.
At this point the Media Director is unusable, so any help would be much appreciated. I'm running an AMD X2 4200+ on a ASUS A8V-MX motherboard with an Nvidia 6200 AGP video card.
Edit: I forgot to mention that I also tried updating the Nvidia drivers to 100.14, but it didn't have any effect.