I think Valky is right.
I had trouble too, but look carefully at the color, and the number and location of the 'stripes' on the equipment slot. For example: with 'systems' the dark blue ones go on motherships and the light blue ones go on fighters. You can't mix and match equipment. Another example: within weapons, there are a different number or configurations of the stripes on the weapon slots and weapons for different types of guns (light, heavy, and so on). You can only put certain kinds of weapons in certain kinds of slots. Once you figure it out, its not so bad. (The mothership can only be reconfigured while its docked.)
Good Luck!
Danya
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