Hi there,
Running UFO AI 2.5 nightly build from 24/04/2014 on Win8.1 (fully updated) 64bits.
After building both missile batteries and laser batteries in the same base, I could not assign more than one weapon system in them despite the 3 slots in each of the buildings.
I had 3 missile launchers in my base and could not assign them to the missile defense (as one per slot). In another base I had 2 laser defenses and could not assign them to different slots of the laser defense building.
In each case I could only assign one of each to the defense building - ie one missile to the missile batterie and one laser to the laser batterie.
Despite that bug, congrats on the 2.5 version, it's probably the best open source game I have ever played.