if you rerun setup.exe some of the entries that could be causing your problems WILL NOT be overwritten. I don't know what you have installed on your computer but this may be a solution for you. (I have used it numerous times without any problems).

In the root directory you will find a file named SYSTEM.1ST - this is a copy of your registry file from whenever you installed Win95. This is a hidden, system, read-only file.
If you replace C:\windows\system.dat with system.1st you will have a fresh registry but you will not have any registry entries for whatever s/w you installed since you originally configured that pc.

don't forget that all registry files must be replace from TRUE DOS.

vlad