Try SFC /SCANNOW from the run line.

Here are some links describing the tool, explains what it does and does not do, and how to use it.

http://support.microsoft.com/kb/310747

http://support.microsoft.com/kb/192832

http://www.updatexp.com/scannow-sfc.html

http://ask-leo.com/what_is_the_syste..._i_run_it.html