just found this post so...
http://i47.tinypic.com/zvxush.jpg - picture showing the bug
It shoots from center of mass and its weapons per bank show up all over the place.

those 2 points in the center are hangers
In the .mesh file THERE IS NO WEAPON 4, but 5 weapons are listed (5x = 0,1,2,3,4)
um.... think Ironclad forgot something....
this is probably why the "planet bombardment seem to be from random points" because its trying to find the correct point to shoot from.
I think 8 points of "Weapon-1" should have been labeled "Weapon-4"
there is also no Bomb point listed and only NumPoints 52
trying to fix this bug but not sure how many weapons to give it checking the manual doesn't help
Weapons (Fore): 6 x Phase Missile Launchers / 6 x Hvy PulseWave Cannons / 4 x Point Defense
Beams / Ship-to-Planet Beam Cannon
Weapons (Side): 3 x Pulse Beam Projectors (Starboard / Port) / 3 x Point Defense Beams
(Starboard / Port)
Weapons (Aft): 1 x Hvy Phase Cannon
6... on a ship with 8 bits hmmmm