When I start Endless Space and try to load a mod (primarily the Colored Anomalies mod but others as well) I usually have to do it 2-3 times before it loads. The first few times I just exit to desktop. Does anyone know what causes this behavior and how I can fix it?

I can suggest to set the game in steam to use the +mod "whatever mod you are trying to load" instead of switching it in game. I too had some problem running mods from inside the game but since i'm almost always running the game with a mod, starting the game with it save a lot of time.

This has always happened to me depending on what is loaded in the background i.e. bittorrent / eve launcher they always cock it up for me