Now, I love me a good conspiracy theory, and I don't want to burst yours, but honestly, HP didn't do anything there, and neither did Microsoft. What happened is very typical Windows behavior. You installed a new mobo and GPU, and then it wouldn't boot the [old] OS. This is very normal and usual behavior for Windows, regardless of the "maker" of the PC. This has to do with the drivers and the registry that Windows creates when you install it on any particular machine.
Providing there was nothing more severe going on, the computer works perfectly on a fresh install of Windows, right?