Some history would be useful.
You could try (re)installing on top of current (rename win.com to something else, then do a normal install booting from floppy with CD support or from 98 install CD. When prompted, choose C:\windows (ie, where existing installation is) not C:\windows.000 or whatever it prompts). This should keep you current installation intact and often sorts problems like yours out, but would rather know how you got where you are before giving definitive advice.