What version of Windows are you running? As far as I know you can schedule ScanDisk/ChkDsk to run on startup. What happens when you do that?
Launch Notepad, and copy/paste the box below into a new text file. Save it as Export.bat and save it on your Desktop.
CODE
regedit /e Output.txt "HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Control\Session Manager"
notepad Output.txt
del /q Output.txt
Locate Export.bat on your Desktop and double-click on it. This will open Notepad with some text in it. Post that.