MoBo install help, software problem?

Ok, here is the story. My phenom proccessor was not compatible with my asus board. Somehow, after 6 months of working, it crapped out on me. It froze up, then would not post. I had the board tested by asus and the chip tested by AMD, both said the products were working. trusting AMD more I got a new Mother board. Bingo, it worked. However, from my info i should have had to either get a new serial number from microsoft, or reinstall windows on my machine ( I have vista 64 ultimate). Here is the wierd part, vista starts up normally as if nothing was replaced. I thought this might be a bad thing so I waited for the other shoe to drop. It did, now any windows application runs slower than a comadore and I can't run any games. The kicker? Resource consumption is below normal for running any of these programs. CPU usage is under 12%, mem usage under 1 GB. Yet if i copy a file to any other location, the transfer file window freezes, thought the file gets copied. Disc clean wont work, but defrag does. It seems to point to the hard drive. Can anyone tell me what is going on, and what i should do? would a format even help?