Not all files are showing up on my network hd, but they are there

I have a PC and Macbook Pro networked in my house using an Airport Extreme. The HD shows up fine on both the PC and Mac (after a bit of problem with the HD format, it is now FAT32).
I have backup software that automatically backs up a bunch of folders. After it finished backing up my music (about 9500 songs) I opened up the HD and only saw folders through D. I switched on the Macbook and it was the same thing. I tried manually adding the folders from my computers HD to the network HD and it said they already existed.
I just plugged the HD directly into my computer (bypassing the network) and all the files are there.
I am wondering how I can get to see all of the files that are on the HD, it is confusing my backup software so that it runs unnecessarily re backing up things that are already on the HD.
Any help would be great

The AirPort Extreme router can read and translate files that can be read on both PCs and Macs when connected to a shared disk. This is an important feature as it allows you to avoid using the very limiting FAT32 file format.
Using FAT32 only makes sense when a hard disk or flash drive is alternately directly connected to both PCs and Macs.

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