I don't understand why they have to be different anyway. I guess they use their native filesystems, though.

Yes, that's the only difference: Macintosh ones are HFS+ and Windows ones are FAT32. Both are "mass-storage class" (or whatever the 1394 word for it is); they appear as external drives. So, unless Apple have gone to the trouble of integrating HFS+ itself into Itunes, you have to use a filesystem your computer's OS supports.

Peter