I read of this right after you posted it. I didn't have to register with anything but the serial numbers that came with the disks. I never had any trouble with the program(s) not accepting them through out the installs. Once each was installed, it would connect to the internet for verification. FSX would anyway. I don't remember if Acceleration did or not.
It seems as if there are remnants on your hard drive though. Somewhere. There is definitely traces of it in the registry though from the sounds of it, that is likely causing the trouble. A good registry cleaning should do the trick. But it sounds like it hasn't.
More curious than anything. Is the drive that FSX was on, a separate drive? Wishful thinking here, because you could just reformat the drive, and then clean out the registry for a fresh start.
If not, all I can think of is that you need to go through the drive by hand and delete/uninstall anything pertaining to, or used by the previous install. Then clean the registry once again. Then pop the FSX disk in and see if it will take.