OK, I'm still not sure if this is a problem relating to the way I set up systems, but every time I try to mount FAT32 partitions on a hard disk, the Finder will mount them in /Volumes, but they will not show up in the "Computer" section of Finder. The workaround for this is simple and I have had no side effects ... yet.

When I was trying to fix this problem, I noticed that at startup (probably when the hard drives mount or fsck_msdos finishes), a file is created for any FAT32 partitions in /Volumes called ._HDNAME (where HDNAME is the name of your FAT32 partition). The thing I noticed was that if I trashed this file and restarted the Finder (not the whole system), the partition would mount correctly. The problem with deleting this file was it was recreated at startup, so what I did was replace it with an empty file that no one had access too, using the following commands:

 % sudo rm /Volumes/._HDNAME
 % touch /Volumes/._HDNAME
 % sudo chmod -rwx /Volumes/._HDNAME
 % sudo chown nobody /Volumes/._HDNAME

Replace HDNAME with the name of your FAT32 partition (which, I think, will always mount in uppercase). This deletes the file that was created (rm), adds a new file with nothing in it (touch), changes the permissions (chmod) and gives ownership to the user called nobody (chown). sudo should ask you for a password the first time (I say should because you can change it, like I have, so it doesn't ask you for a password).

This fix has been tested on 10.2 and 10.3.