i think i know what is wrong...
have a look:
FAT32
! Hermes cIOS 222/223 or waninkoko's rev19 must be installed to use FAT32 !
PRO
Can be used for other files
Ripping to FAT32 is possible
Widely supported by many OS
CON
Only files up to 4GB are supported, so bigger games must be split up (note that games can be scrubbed, so most of them won't be over 4GB)
Only supported by 2 Loaders and few WBFS managers
If you choose FAT32, you won't have the problem that you can't put other files on the drive, since FAT32 is widely supported.
The only problem you'll find is the addition of games to the drive. It is possible to read .ISO files directly from the partition, but due the 4B limit of FAT32 it is often impossible to put the ISO (which are usually around 4.37GB) on the drive. Instead, the games must be converted to .wbfs files, which can be split up if they are bigger than 4GB. Because of the automatic scrubbing of .wbfs files, most games will stay under 4GB so it won't be that much of a problem.
To do this, you will need a backup manager that supports converting to .wbfs files. Currently, these are Wii Backup Manager and Wii Game Manager.
NTFS
! Hermes cIOS 222/223 must be installed to use NTFS !
PRO
Can be used for other files
Supports bigger files, so ISO loading is possible
CON
Ripping to NTFS is very unstable. It is highly recommended to add your games with your computer.
Only supported by 2 Loaders and few WBFS managers
As with FAT32, the problem of not being able to use the drive for other things is not present on NTFS. On top of that, it also supports files that are bigger than 4GB, so ISO files can be put on it directly.
It is NOT possible to rip games to NTFS with a backup launcher, so you'll have to use your computer to add games to the drive.