Matt,
Yeah, given Windows limitation of 32GB while formatting FAT32 partitions, you'd have to work around that. Microsoft suggests formatting in another OS (your OSX box should do the job perfectly). To do it in DOS would require a boot disk that loads the USB or Firewire drivers so you can access the drive, or you could remove it from the case and connect it directly to an IDE interface. Hopefully there's no crazy limitation like this from within a DOS version of fdisk and format.
Good luck!
- Jason