X:CE 0.31 Mod Management: All Non-XCE Mods Deactivate upon Installation of New Mods

I am using the Non-Steam Version of Xenonauts v1.09 with the latest version of XCE (0.31) of which I downloaded from the forums on Dec/9/2014.

Step 1 - Install X:CE 0.31 using the "Modding Tools" part of the Xenonauts v1.09 Launcher then close the launcher.

Step 2 - Open XCE's Launcher from it's file in "/mods/".

Step 3 - Go into the "Modding Tools" section of XCE's Launcher and install a few mods such as "Armoured Assault!", "MagFromVenthe", and "NewLasers_v0_2".

Step 4 - Activate all of the currently installed mods and then proceed to install another mod such as "Fire in The Hole".

Result - All Non-XCE mods will be deactivated and the latest installed mod will be auto-activated.

You are right with that. I have the Steam Version and i noticed the same. I play the big one XnT-Mod and he is automaticly activatet. The XCE-Mods which are in the Mod folder you can choose Yes/No.

I play only one big Mod with all integrations of much other mods (XnT), so that Problem dosen´t matter me much. But I have the feeling, that they want you can only play the integratet XCE-Improvements and one Mod like in much other Games.

But without XCE-Improvements the most Mods would´t work. Maybe it is a Bug but I think its a Feature.