cpu running low, computer freezing (vista)?

Last week I was playing Flight simulator during a thunderstorm. The computer I was on is NOT connected to internet at all. Lightning hit really close, knocked out power for about 5 seconds shutting off the computer, then restarted. Before the lightning it ran fine, but now it's running weird. When I click something it sits frozen for about 30 seconds up to 2 minutes sometimes, the running at about 2-4%. You can even hear that the computer stops running, and then it starts after a while. Then it wakes up and runs fine until I click something again. My temps are fine, about 35-40*C, memory seems fines, everything shows working properly according to the device manager. No errors that I can tell. The only thing I think it could be is when I run chkdsk (which I have about 5 times since this startd happening), There are 8 "unreadable" sectors. these are 562072-5 and sectors 796752-5. It says they are unreadable but doesn't fix them. They also trigger an error when i run a system diagnostics
in the perfmon. I have a Athlon 3800+ Orleans, 2.4Ghz 1Gb memory, Asus A8m2n-LA motherboard runnin Vista Home Premium.