I had/have the same problem with the newest drivers. I just uninstalled everything AMD related I could find. Use this guide. Then I let windows install the drivers it has which is Catalyst 13 and things seem to be back the way I want them. I'm hoping this is a bug and not feature.
Same problem - screens switched around - black borders - system going so slow
System restore worked for me
First time I've had to do a system restore on this system in 4 years!
XFX Radeon HD 5870
MSI X58 Intel i7
Windows 7 Ultimate 64-bit
Screen 1 1280*1024 DL-DVI
Screen 2 1920*1080 DL-DVI
Screen 3 1920*1080 DP (Active adapter to HDMI TV)