What ISP do you use? They may be throttling your speed if they notice bittorrent traffic. I've not had a problem using BT on BT Internet. Try checking the box "prefer encrypted peers", also using Distributed Hash Tables, and PEX. Make sure there are no bandwidth caps in place either.
I'm on virgin media, reports say they don't limit bittorrent traffic but if you go over a limit, they put your speed down overall, I've checked with speedtest and my speed is the same as it was before. I've taken off all caps on bandwidth, I only had them on upload and it was set pretty high. I don't have the rest of the options because transmission is a pretty lightweight, simple program.