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My laptop dual boots into XP and 98. Recently, my 98 partition comes up with, "Windows security error, reinstall windows" or something along those lines. In the past, when this showed up on other computers I was able to fix it by removing a new .inf in one case, and having to reinstall in another. Is there some utility that can detect the problem and fix it? I don't want to reinstall. (I really can't, actually)

That's an odd one. Makes me think some malware may be involved. If possible, post back the exact wording.

go to run line, type in
msconfig
open startup
uncheck everything there but systray.
that popup will go away.
it is malware

What, in DOS? I can't start windows. I don't know how malware could have got there, the laptop doesn't go online, and I've had that on computers that don't even touch the internet or other computers.

Oh, one other thing. It may be difficult to get the exact message because my laptop's backlight doesn't come on when I start it up. In XP I solve it by (sometimes repeatedly) pressing the standby activator. However, in windows 98, it turns the computer off because it won't go into standby when booting.

Not much info flowing here with which to isolate the problem but anyway:
As far as I know, 'windows security error' is not a message from the OS and is likely coming from some added software. For that you'd need to review what software you have loaded and see if that message applies to any of them.
'Windows Protection Error' is coming from the OS but is not usually a simple fix. You can google "windows protection error" and see if any of the links help.
Possibly you could revert back to a previous registry from before you had the problem. Boot to dos by tapping F8 before the OS starts to load. Choose 'command prompt only' from the menu. Then at the prompt type scanreg/restore and enter. Choose a registry to restore with a date that precedes the problem.

Unfortunately there's no straight-forward fix for that. Sometimes the message will give some details that will help. Also, I've never heard of any diagnostic software that will help. If you can get to safe mode via the F8 menu you may be able to delve into it more. Did you try scanreg/restore?

Oldman have you installed any new software before this happen? Once in the past when I installed this one software a virus was set loose on my HD.
You have two OS running on one HD?

Two OS'es on two different partitions. I ran scanreg, but apparently I deleted the autoexec bat or something because it says wrong system disk. I'll try sys'ing the HDD, maybe it'll run then.

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