According to this topic:

http://www.gametracker.com/forums/forum.php?site=1&thread=56450

GT doesn't care about non-steam servers because it can't detect it with simple methods. Well I've come up with a sure-fire way to detect it with a very simple code. If you are really interested in deranking non-steam servers just PM me and I'll provide the code but I don't want to share it here. If you are not into deranking them, still reply please.

Deranking non-steam servers has been on the todo list, but it is not a high priority at all unfortunately because it is hardly that serious of a change for the website.