I had the same thing happen once, never did figure it out. So I re-installed and it went away.
You can use fdisk from a 98se boot disk to get rid of an NTFS partition, it just reads it as non-DOS. I do it all the time. You cannot however format in NTFS with a 98 boot floppy.
So if ya want to try re-installing Xp. Backup anything ya need from the Xp install. Boot with a 98se(not sure if plain 98 will do, haven't tried it)bootdisk and clear out all the unwanted partitions, set them up as you like. If possible boot Xp install from the CD(goes much faster this way)then select the partitions you want in NTFS and format(quick format sucks) them. See if it fixes your problem/curious behavior.
Good luck.