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.
So you're saying install 2.6 first, then a pre-12.1 driver? or 2.6 and THEN 12.1? I'm noticing that it is 'overwriting' something because it actually deletes the 2.1 kernel but doesn't replace it.
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The linux 2.6 README.txt says that.
So in linux if you want to use a specific fglrx driver there is a catch:
Installing SDK 2.6 writes over the current fglrx driver - so you have to install the fglrx driver AFTER SDK 2.6 (or re-install the fglrx driver)
The docs saying >= 12.1 just means they don't want you running something older than the driver they added in 2.6 SDK has (which at a guess is probably something like 12.0)
Thus if you install old < 12.1 driver, then SDK 2.6, the SDK will update the driver.
If you want new >= 12.1 driver you must install the driver AFTER the 2.6 SDK.
Again - this is all how it works on linux but I guess it could be the same on windows