Turning on protocol encryption sounds inefficient, but it resolved my problem. I suggest turning it or at least make it optional. This one was tricky to troubleshoot because some ISPs don't care about P2P traffic all that much and seeding non-baka bt torrents was going swell. But some peers may not be as fortunate and have to use other means getting around the potential problems of throttling. When the number of peers dwindle and appear from places I haven't even heard of before, this can make a big difference in one's potential capability of seeding.
If this is not in the FAQ or wiki for beginners, this might be a nice hint.