Plan A: You can perform a reinstall without impacting any installed software. The Win98 install process relinks your previously-installed applications and leaves your system 99.5% the same as before the reinstall. Surprisingly often, that 0.5% change is the gunk that was messing up your system.
Plan B: Only if this does not work, you probably do need to reformat your disk and do a "bare-metal" rebuild. But this will require full reload of all applications, and the loss of all of your old data.
Definitely try Plan A before giving up and going for Plan B.