You need to edit the Boot.ini file and remove it from there.
You can use the following command:
go to a command prompt and type, boot.ini -r -h
the -r gets rid of read only and the -h removes hidden attributes. Then from note pad just open the boot.ini. Under
[OPERATING SYSTEMS] remove the line that corresponds to the win98. Then save
Once you have done that. go back to a command prompt (Before you reboot) and type, boot.ini +r +h to put the attributes back.(Very important)
BEFORE YOU DO THIS, make sure your Emergency Repair Disk is updated.