Using the weapon AI, I was able to see the following things: If you set the commands to attack a specific room in two equal conditions, neither of them will activate. Maybe it's random, but it happened to me every time.
If you set the attack commands in a room and want only that room to be attacked, you have to set commands for rooms that don't exist on the enemy ship.
If you set the command "the enemy room has less than half its health" on a single weapon but for different rooms, the commands won't follow the order and may overlap each other.
Setting the commands "the enemy ship has more than half its health" and "the enemy ship has full HP" will make neither of the two commands work, your weapon will not fire (I lost a defense discovering this, when I looked at the replay I analyzed it and then confirmed that it was that).
I'm seeing more things at the moment, every time I discover something I'll post it here...

