as you will be aware, linux creates a bootfile which enables you to choose which O/S to boot into. (grub or lilo)
windows xp when installed with win98 also creates a bootfile (boot.ini) on the c: drive
could you give us some more info regarding drives/partitions. what boot options you get at startup?
what version of partition manager?
from my experience, win98 should be on drive C:, XP on drive D: and linux on drive E: (though it wont be drive E in linux, probably hdb1 or hda5 etc...
would you be prepared to format the linux partitions and re-install?
it seems like you are having a conflict with the boot options.