Changing the mode of the hard disk, usually means windows does not boot up at all anymore. These steps allow the boot to take place anyway and windows to work, but, it has to swap out drivers and so on, and things can go wrong there. So I suspect this is the reason.
I wonder why you changed the mode... It's not like you'll have much benefit, but oh well. Probably the only way to fix it is a fresh windows install. You can try reverting back, but I doubt that will fix it.