The main thing that comes to mind when I hear things like this is, did you format Windows before sticking an AMD card in? I always format before switching from AMD to Nvidia or vice versa, never have issues. Surely it cannot be PEBCAK as sugested by Humbug as you are competent enough to build a custom cooled PC. Apart from that it must be bad luck
What? you reinstall everything when you switch GPU? That hasn't been needed since windows 7 was launched. You can even swap motherboards now without issues. Reinstalling the operating system when changing hardware is a hold over from the days of XP and older operating systems.
It might not be PEBKAC or bad luck, it might be all down to perception. People tend to be a lot more tolerant of issues for a brand they prefer, whether it be mobile phones, cars or graphic cards.