uhm... well, maybe you can place the files on the fat32 disk directly instead of first downloading them and then move
dunno what version of transmission raas is using... probably the newest version (one with some fancy buttons and upload a torrent file screen etc.)
You can most likely change some things to copy it, or build a cron job to scan the active jobs (and when one is done) cp them to a different drive..
depends a bit on what version of transmission you are using
transmission is quite slow anyway, ntorrent goes way faster (up to 2.7mb/s easily)
btw, it's EXT3 on oleg