Maybe it would've been better if you didn't uninstall the channel (and instead went with the alternative registry solution in the note at the end). Oh well, too late now.
Your system is still stuck in PIO mode, and from your description, I'm starting to think that you're using a 3rd party driver here.
Check the drivers used for your channels and for your IDE controller. You should be using Micrsoft drivers. If you are using drivers from another company (Intel, for example), uninstall them. You should never use anything other than the default Microsoft drivers. The so-called improved performance of things like Intel's Application Accelerator is more or less snake-oil and often just causes problems.
What probably happened is that because you were using 3rd-party IDE contoller/channel drivers, the SP2 upgrade probably triggered some kind of compatibility problem that kicked you into PIO mode. Another reason to use the default drivers that come with Windows.