When loading Windows 98SE I get the dreaded blue screen of death twice and then windows loads fine. Now I am assuming this is a driver problem with one of the drivers it is loading on startup. Is there any way of finding out which driver is causing this problem.
Seeing as you can get into Windows try clicking on Start>Run then type sfc then click OK. This will have an option to run a complete System File Check so Windows will check itself and any files that are missing it will ask for the Windows 98SE CD ROM, so be read to feed it.
The other alterative is to re-load Windows over the old one, again it will replace anything that is missing, but it's a bit more long winded.