The linux 2.6 overrides two of the main ATI drivers.
(libaticalcl.so  libaticalrt.so) and the README.txt tells you to install any 12.1 driver AFTER the 2.6 SDK (since it overwrites those 2 files and they obviously must be pre 12.1)
So there may well be a similar issue on windows - but of course I don't know since I don't mine on windows.