to open a dos windows within windows98, open your run box/window thingy and type command - that'll open a dos window.... if it won't allow you (as u mentioned already i think) to run scanreg within windows do the following...
1. Exit the MS-DOS window, single click on "Start."
2. Single click on "Shut Down...," single click on "Restart the computer in MS-DOS Mode."
3. Single click on "OK."
The computer will restart in MS-DOS Mode. At the "C" prompt (C:\), change to the DOS application directory and type the name of the .exe file and press <Enter>. (info from here)
This page seems to have a good guide to diagnosing startup problems too, if a) you can slot in a look between poker games and B) Mick hasn't been over to do that burial thing already
good luck