Well, you need to be more specific with this problem.
If you're rebooting your computer which *already* had Win98 installed on it, it shouldn't be rebooting into the "Set-Up Mode" (I assume you mean Windows Setup?).
If this isn't it, what exactly are you talking about? Product name? Splash screen? Know if any extra peripherals (like Centurion Guard or something) are installed? Any third-party disklockers?
I'd be more than happy to help if I knew what to help with.
For now, all I can suggest is that immediately after you turn your computer on, start pressing "F8" - this should kick you into Safe Mode. You should be able to at least poke around then and see what's up. If that's not even possible, well...get back to me.