Ok:
you created a fat32 partition under Win2000
you mounted the partition under Fedora and created a folder
you can see only the folder in Win2000, but not the other files on the partition
Is that correct?
If so, I'm missing a step "created more files/folders on the partition in Fedora/Win2000"..
Anyway, check what attributes the other files/folders have, it could simply be that the folder is for example hidden.
Step 2:
Post here what you get when you do "ls -lsa" in your mounted fat32 partition under Fedora.