So, I have been playing Sins of a Solar Empire for about a year, and I have come across a particular problem quite a few times and this problem always makes me quit my games in frustration. 

The problem is this, when I create my Cap Ship right after the game/match starts it gets put on the Top Left corner of the empire tree. This is good because if I hotkey it, it selects the Cap ship and not any other frigate that I make. However recently I have been getting this problem more and more. The Problem in Question is this, When I create any kind of ship after I built my first Capital Ship, those ships come BEFORE the capital ship in the empire tree. I find this really annoying because when I hotkey and make a fleet, Instead of selecting the Capital Ship which is the flagship, it selects the Frigates/Cruisers before in the empire tree. 

For those of you who don't understand me - http://i50.tinypic.com/15ho86v.png

I have no Idea how to get rid of this problem, so if anyone knows what this is, I would appreciate you helping me because I really hate this problem as it makes me basically quit my game. Also I am playing the Distant Stars Mod, but I have seen this problem in the Vanilla Diplomacy 1.34.