Point, click, crash!!!

this whole thing started when i was forced to restart my computer because it crashed when i was playin quake 3.
Im runnin win XP Pro and when it got to that white loading bar at startup i got the error message

“C:\windows\system32\config\sysytem is damaged” and so on…

so i boot into dos and repalced the damaged system file from the c:\windows\repair folder. This seemed to work and i managed to boot back into windows, i did have to re-install my modem drives and change some other stuff back to normal.
This is the second time this has happened to me and i was wondering if anyone else was any the wise of this problem?
I think it might be somthin to do with my sound card as i keep gettin a distorted start up sound which sometimes locks the whole computer up with a loud high pitched squeak!!!