When accessing over a network, thats fine. If booting with FAT32 and accessing a slave HDD in the SAME computer (not over a network) FAT32 is unable to recognize a NTFS table. Now, if you boot NTFS, u can read a FAT32, but not vice-a versa unless done from a network (like computer A can access data on computer B, its a part of the network model. Its like a small gateway in your system (not really, but its the closest I can think of). You may of installed something on a local system that has the secondary function of reading other file tables and not realized it because you use this for its main function. Anyhow, on a normal system it is not possible. Check out microsoft.com and do a lookup on it. Now when I say 'local' I mean the HDD that is in the same computer. So, to make it short, here is what it looks like you are saying:
You have 2 pc's A and B both are win9x with FAT32... so...
A = FAT32
B = FAT32
A and B are on a network
you have another PC we'll call C it has 2 partitions that uses NTFS
(A) FAT32
(C)NTFS
(B) FAT32
A and B can access C because they are accessing it via the network. C can access itself since, well, it's NTFS. Now, if it were like this:
(A) FAT32 <boot> NTFS 2nd drive
(C)NTFS
(B) FAT32
then computer A can boot and read computer C's NTFS, but can NOT read its own 2nd drive. Computer B can read both A and C (over a network). A cant because its local, OR is located on the SAME computer. You've got to remember that when accessing over a network you have alot of data interpretation going on, and the hardware in the computer will interpret what it needs. When accessing a drive in you're own system, though, its using its own logic to try and read something with out a interpreter.