System File Checker or SFC will run against you windows files and check that they are correct and accounted for. It does more but hopefully that will suffice.
There are 3 options I'm interested in to run it are
The SfcScan values are set in the following registry key's
0x0 = do not scan protected files after restart. (Default value)
0x1 = scan all protected files after every restart (set if sfc /scanboot is run).
0x2 = scan all protected files one time after a restart (set if sfc /scanonce is run).