I think this may somehow be related...
A couple of days ago I made a small ship for the pirates armed pretty heavily with heat-seeking missiles. I wanted to test a few things out (for example seeing if pirates could use missiles since I\'ve been having issues with turrets not firing missiles). This was all done on a multiplayer server. Anyways, for \"safety\" purposes I decided to test it by spawning it right above our planetary base, which was heavily defended by lots of ships and AMC turrets. As soon as the pirate spawned he fired a salvo of missiles at me - wonderful! It works!
However, within seconds my joy turned to absolute horror, dismay, and shock as the \"little\" pirate ship (about 115 mass) suddenly began firing salvos of missiles repeatedly! The reload time should have been every 17 seconds, but this bugger was firing them off faster than the grand finale at a fireworks show! It seemed that every time it got hit by laser fire from our turrets it would fire off another mass of missiles. I\'m guessing, as you noted, that every time a missile group was changed (blocks being destroyed by laser fire) it would reset the timer for reloading.
Eventually the \"little\" pirate ship was destroyed, but unfortunately not before it did massive and unholy amounts of damage to ships that were stationed in orbit. Somehow (or not) the massive barage of missiles overwhelmed the shields of a powerful warship that belonged to my friend and completely destroyed half of his ship. He was not happy! As you may have guessed we immediately removed this ship from being useable by the pirates until this issue can be resolved...