It is a shorter than a normal in-place Upgrade because it is leaving everything exactly in place except reinstalling the OS, and (really important here) reconfiguring the boot.
I have had it solve almost any problem, except in some cases it can carry over already-existing corruption in programs, files or settings but it will not allow any to remain in system files which are all replaced.
I think this is the best possible thing to happen because anything past which was a problem, or created just now with the moving operation has a very good chance of being ironed out completely.
Believe it or not, I was ready to recommend you a Repair install much earlier but thought we should wait until you jumped your Win7 drive over the huge data drive into first partition. That's how it turned out, too.
I need to go to bed now