One thing I have noticed is that when using a missile weapon against a creature that has got you targeted as primary (at range) you seem to develop a -2 to hit penalty.
Essentially what this means is that your first shot is at maximum AB (when the creature is unaware of your presence), and then all other shots as long as that creature is coming at you are at -2 off your AB.
I know this isn't part of the NWN or D&D core rules, so is this a special mod that was developed for EFU:A or is it a bug?
If they're moving, missile weapons are at -2. It's normal.
What Egon says is confirmed in the NWN Wiki article on ranged weapons.
http://nwn.wikia.com/wiki/Ranged_weapon
Not a bug.