xp installation repair

Hello,
We have a computer that was infected with viruses. The effect of the virus was never really resovled We got an error that the “rundll.exe” file could not be found although it was. We tried do a repair with the ultimate boot cd because we had no recovery cd from the pc. The recovery process did not function properly because we now have two operating systems one that work properly and one that dosent. the other problem is the one that works we can activate nor do all the programs work.

im sorry i have written so much and i hope i have described the throughly enough to understand thanks