I've seen the Cherry software do weird things, such as block the PS/2 keyboard that was connected because my Cherry keyboard was connected via USB. Works fine to log in, then boom, nothing.
From what I have been able to gather, this is a holdover from when the card readers were PS/2. Allow them to be used for login, then lock them out was apparently the norm.
Anyway, I agree with what others have said, and it's unlikely anything to do with the keyboard, either the swapping or the software itself.
What's more likely is that installing the software corrupted something on your drive, or was written to a corrupt location, and being in the Windows directory caused the inability to boot. I'm betting the problem is the boot drive, not the other hardware.