I will try to help. Before we start I want to apologize for my bad English. What are your speeds?
You should run speedtest with your computer connected directly to your modem at different times of the day. You should take note of the lowest ever values of speeds that you get. you should then use 85% of those values. This is important. Don't use your whole bandwidth as it will break QoS. Read this thread on the subject: http://www.linksysinfo.org/index.php?threads/using-qos-tutorial-and-discussion.28349/
To sum it up, this is not real QoS. It's traffic shaping and you are doing it only at your end. Since you have limited control of your bandwidth, you must make sure no traffic ever gets queued at your ISP. The moment a queue is formed there, your ping will sky rocket.
The other issue is that Dlink QoS does not have default rules. This means that all devices must be in a rule somewhere. If you just set your seedbox to low priority it will not work. You must set some priority to all other devices in your network.
Are you on the latest firmware available? Check to see if there are any updates on the Dlink website.
Try these tips and get back to me if that doesn't work.
Edit: Looking at the image you poted, I think you should use Weighted Fair Queue instead of strict priority. I'm pretty certain it uses HTB under the hood.
The "Application Port" under the "Classification Rules" - I guess this is an arbitrary text box where you can type in custom or preset rule definitions? What is in your "ALL" definition? – Kinnectus – 2015-08-25T06:45:31.820
That is the default setting. I want the entire system throttled, not just p2p. – Christopher Markieta – 2015-08-25T07:25:45.740
I have tried specifying the port for Transmission and lowering my uplink, but it still doesn't seem to work. – Christopher Markieta – 2015-08-26T01:40:16.823
You may want to consider backing up the configuration and factory resetting the router and try the QoS settings from a clean slate... – Kinnectus – 2015-08-26T07:26:33.723