Ah just checked after you guys said that and the stick that wasn't working was just FAT and the stick that is working is FAT 32. Thanks for your help guys, I'm really pleased that it does work, it seemed utterly pointless to not be able to read files from a USB stick. Really didn't want to have my phone running all the time if I could help it.
You posted the model of your headunit, and the manual is available here, and page 21 lists: Unless I'm reading wrong, your head unit should support MP3, FLAC, and WMA only.