You could also check your /etc/fstab file for the settings on your floppy drive as follows:
/dev/fd0 /mnt/floppy auto noauto, owner, kudzu 0 0

The 'auto' in the 3rd column specifies the file type, In this case it will detect any of the file types that have been compiled into the kernel. For example, ext2, ext3, fat, vfat, iso9660,etc. This should allow linux and windows to both read the floppy. For a complete description of the /etc/fstab file do a "man fstab" in a terminal windows next time you are in linux.