Windows Shutdown Problem

When shutting down Windows the computer is powered down automatically, but the keyboard lights are staying on. Also, when starting up Windows I am prompted with the message about Windows not shut down properly, run scandisk… BIOS settings have been checked, the hard drive was formatted and Windows was reinstalled. Everything worked okay for about 2 days but then problem described above starting happening again. This is driving me crazy! Does anybody have any suggestions as how to fix this problem? Has anyone seen this problem before and know how to fix it?