3 hours? Well how many files you move how many files you add, alone for me at 2% Fragmentation Windows Defrager takes 20 minutes. Defraggler is about the same, also did you restart, were these files large small.. Everything you do on a computer hard drive causes fragmentation, even your computer idling causes fragmentation thanks to page files. Even a restart causes fragmentation, of course all that is really small did you happen to see how many fragments there were, anything thats helpful besides how long it took and the fact you canceled it?
Also did you try Windows Defrager after the fact or leave all the fragmented files..