The command to run the file system integrity checker is "sfc /scannow", not "scannow". If you are typing in the command just like that, it's possible that your path is messed up. You can get around this by typing in the full path to the program. If your Windows folder is in the C:, you can run the programs like so:
C:\WINDOWS\SYSTEM32\chkdsk /r
C:\WINDOWS\SYSTEM32\sfc /scannow
If those still don't work, your system may have serious file system issue or have a very nasty virus that is removing files. You have one last chance to try to fix the problem without reinstalling Windows. You should be able to run those programs directly off of the Windows install disk. If your Windows install disk is loaded in your D:, you can run the programs like so:
D:\chkdsk /r
D:\sfc /scannow
If this also fails, you will most likely have to reinstall Windows.