That sounds like the problem I encountered in my last sysprep transfer. It also suggested I use the install disk and try to repair the installation. I wish I could have known of this little trick, as I would have liked to try it. The repair found and repaired a problem with the boot, but even after that it was unable to repair whatever was wrong and it actually gave up. So did I, so I just re-installed. No big deal in this case, as the pc is secondary and gets very limited use. But I hate having to go through all those updates again!
I'll keep this tip handy in case I need it in the future. Funny, I expected problems when going from an Intel combo to an AMD, but that transfer worked without a single problem. Didn't even have to re-activate...with an OEM retail version!