It's probably traffic shaping by your ISP that is causing the slow speeds. Protocol encryption will work on hardly any ISPs now, since they've wised up and are using deep packet inspection now. If it's shaping, you probably don't have any option other than to switch ISPs.
Having said that, if it does fix the problem, you can prevent it from limiting the number of seeds by increasing the number of connections allowed per torrent and allowing connections from non-encrypted seeds.
You may also want to try changing the port which your client is using, since some ISPs blacklist commonly used bittorrent ports.

It could also be a NAT error, which is caused by traffic not being routed to the correct internal IP (or ports not being forwarded), resulting in the client only receiving about 10% of the packets sent. You need to find out where the traffic is being blocked in your network - It could be your router, hardware or software firewalls - and make sure that all ports are forwarded on the right internal addresses. Note that for port forwarding, you generally need to set static IPs on the machines you want to forward the ports for.