If you select NOT to download all files of a torrent's file list, you never get 100% of all files and can't be a seeder. So the tracker will count you into the downloading peers. Of course the data which you upload will count towards your upload.

@addidasjock: Looking through the torrents seeded, it appears that low upload rates are due to missing downloading peers. I've made 5 torrents out of them with a low seed number freeleech. If missing downloading peers are the issue, you should see soon a short spike in your upload rate.