I've had a ton of issues after installing the AMD/ATI drivers on 12.10. I had to follow some workarounds to even get my system to boot.
Now that I've got drivers installed and my dual monitors set up, Ubuntu puts the launcher on the secondary monitor. When I try to switch it in Settings -> Displays, I get a couple of error screens.
I got the first message when I tried to configure my monitors through Displays, but realized I'm supposed to do that through the Catalyst Control Center. Unfortunately, there's no option in CCC to switch launcher position.
The launcher moves over after the errors but reverts back after a restart.