I have Windows98.  I tried running WinnowCleaner and now Windows will not start.  I tried a start up disk, did the sys C: which transferred. I restarted and the windows picture showed but WENT into the c: prompt.
The only function that seems to work is the DIR.  Can I do anything else or do I need to reinstall Windows? PeteCheck Your C:\msdos.sys file
Check where is the Windows system directory.
It may be C:\Windows...
the content at least:

[paths]
Windir=C:\windows
WinBootDir=C:\Windows
HotWinBootDrv=C

[Option]
BootMulti=1
BootGUI=1

Where "C:\Windows" is system directory.

You can use a text editor to edit the above line in your msdos.sys file.
Run the COMMAND "Scanreg.exe /restore" this file is existed in Windows\command
Command "Scanreg /restore" help you to restore your Windows registry.
The Syntax like below
C:\scanreg /restore
then CHOOSE the registry backup file base on the day it created and then ok.....
Hope this can resolve your problem!

   
Did u use the win command in the C: prompt? That should do something.