Hard to say. You haven't said much about your hardware. It's possible there could be a hardware issue on your end but I doubt it.
Since I don't use the peer apps, I can't comment on how to tweak them to get the best speed. I would imagine the issue you are seeing is more related to the application and it's use of the stack. Are there some good studies of bittorrent, how it handles acknowledgements, frame size implications, etc.? If so, you might need to do some research to make effective use of the pipe you have.