Have you tried deleting the partitions first?
Use a Windows 98 boot diskette that has the program fdisk. Use fdisk to delete all partitions, then make a primary partition of whatever size you want, then an extended partition with a logical DOS drive.
After you have created the partitions, then reboot the machine, boot with the floppy again, and format the partitions "format C:\" and "format D:\"
This will format them as FAT32. If you try to format with FAT32 overtop of a NTFS partition without deleting the partition first you will have problems.
HTH
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