Some thoughts...
You used a '98 boot-disk to format the HD - did you set it to FAT32???
If so then that's part of the problem...
Start over after running Fdisk on the '98 boot-disk to remove all partitions; do not re-establish any. When using NT set-up (floppies or booting from the CD, if possible...) you can select and configure partitions on the HD as you prefer... I suggest you have at least two - a Primary for NT OS itself and an Extended area for data etc...
If your HD is larger than 7.8Gig you will also need to address that issue too.
Visit John Savill's FAQ's at:
http://www.windows2000faq.com
(part of http://www.win2000mag.com)
Installations section; and browse for relevant item (using HD's larger than 7.8Gig); he gives you all the relevant info...