Win 98 can be a pain. Try running Scandisk from a floppy. If that doesn't work, try running a registry check program from a boot disk. It has to be either a missing .dll or registry entry.
If all else fails, and you're sure someone just did one thing to the computer, you could probably run the Win 98 setup CD after booting with a boot disk and run an install over the top of your current 98 install (if it doesn't give you a choice to repair the current installation; can't remember if it does).
Good Luck.