Computer not recognizing cloned hard drive

Hello,
I bought my son a used dell optiplex gx620 computer, I took the original 80g hard drive added acronis to it and cloned it to a 250g hd, I do this on all my computers, so if he gets a virus I just clone over it. I leave the original hard drive unplugged in the tower. Well my son got a virus, that wonderful xp 2011 virus, I couldn't boot into safe mode and run maleware bytes, no go. I hooked up the clean hd, put his infected one as secondary plugged into sata 1 spot. Computer will not see that hard drive as a secondary at all , each one will boot up fine by itself. I swapped cables just in case, both cables work in sata 0 and 1 , tried swapping 2nd hd to sata 2, sata 3 will NOT see it. Any suggestions?