These are the specs on the system I am using:
(A little lame nowadays but whatcha gonna do?)
Celeron 300A OC @ 450MHz
128MB PC100 SDRAM
40x CD-ROM
8x4x24 CD-RW
3GB Master Drive with a 1 GB partition [C:] and a 2 GB partition [hidden?]
40GB Slave Drive
Windows 98

I have Windows 98 installed on the 1GB partition [C:], and was planning to install Linux on the 2GB partition. However, the 2GB partition doesnt seem to be there. If I run FDISK I can see it but once I exit FDISK I cant.

Does anyone know how to make the second partition visible and usable?

Try format d: - a partition must be formatted before you can see it

Maybe you should unhook your 40gb slave drive first sorry didnt see that
or format e: so you dont delete your 40g

:o

If you have different filesystemt on the different partitions, they might not be able to see each other.
I have run into to this problem several times, when i have had both win2k and 98 installed. The FAT32 partitions could not see the NTFS partitions.