Thanks guys. That is in fact what I did. I was thinking that if linux detected the drive that it would prep it automatically. Especially when it was copying files <4.2Gb. I formatted the drive and it works like I would expect.
The trouble with prepping drives automaticly is that there might be data on the drive that you would actually like to keep... like your media for instance. I can still vividly remember the day that somebody else's windowsCE decided to automaticly "prep" my ext2 formatted pcmcia HD, took me days to get my files back.