Vista - filesystem error

After installing Vista SP1, with no apparent problems, I keep getting this
message when AVG Free Ed. runs its daily check. No virus has been found, or
spy/malware either.
kernel32.dll, wsock32.dll, user32.dll, shell32.dll,and ntoskrnl.exe are
listed every time as changed. When I do a chkdsk on C:, it says there are
errors, and I tell it to run and repair the file on the next boot, but the
next AV check says the files are still changed.
I'm assuming it's something to do with SP1, but how can I get the system to
recognize the changes and quit reporting this as a problem.