I think their might be a problem with the Pulsar Beam weapon. (or maybe its a game mechanic that i am unaware of).
I often see the following situation:
Ships with full elite crew (i almost always run with elite crew only so i am unsure if it happens with less experienced crew as well). Having equiped a longer range weapon (then the pulsar beam), i often see them circling an enemy firing all weapons, however they are at the max range their heavy weapon allows, this means that even though its firing the pulsar beams at its target, its never hitting it. Thus wasting flux.
For example. I currently have Rathar class destroyer, fitted with an sequenced pulsar and 4 pulsar beams. Its always trying to be at the max range the seq pul. allows, however its pul beams are always out of range of its main target, yet they are firing.
Not sure if this is a game mechanic/limitation, or maybe there is something wrong in the definition files of the weapons thats causing it.