Pro Upgrade to SP 2, maybe Linux Interference?

Hi, not too long ago, I reinstalled XP Pro on my computer and I found that I
couldn't upgrade to SP 2. I had an installation of Ubuntu 6.06 running off of
an external hdd that was connected to my computer, and I think the pattern
has been, whenever I have had that connected, the Windows Update always
freezes when checking for my product key. My key is fine and it has worked in
a past installation or two, I think when I have not had that Linux
installation at all introduced to the system. I think I can fix the problem
by redoing everything, but I would really rather not if it can be avoided. Is
it possible that Linux maybe reorganized files or something like that so that
Windows doesn't quite know where to find it? If anyone has any possible fix
ideas, I would really appreciate it. Thank you very much.