Hi Zodiac,
this is most likely because your harddisk is formatted as NTFS, while the boot disk you use is can only recognise FAT partition.
Note: there are a few types of partition format. win98 can use either FAT16 or FAT32. WinNT is using either NTFS or HPFS. Win98 is not unalble to read NTFS nor HPFS format.
You will need to get an NTFS boot disk and try to boot up with it. You can either create an NTFS bootdisk from a windows 2000 computer or try to create 1 using resources from the internet.
cheers