My 2c: this sounds like a movement initiative problem. This is how I believe it works (sorry in advance for the lecturing tone if you already know this!):
if you look below the speed settings in the task group orders (f12) screen you'll notice that every task group has a rated maximum and current initiative. Initiative determines the move order, with (IIRC) lower initiatives moving first.
so let's say task group A, moving at 10,000 km/s is trying to close to zero range on task group B, moving at 5,000 km/s. but task group A has worse initiative.
task group A determines the location of task group B and moves to zero range.
task group B, having better initiative, notes that task group A is now at zero range and moves away at its best speed, ending up 25,000km away.
the end result is that despite task group A having a huge speed advantage, it can't get any closer than 25,000 km (the range at which task group B can move in 5 seconds.)
this phenomenon means that any weapon that depends on being 10,000km away from its target or less is kind of terrible against any kinda ship :^)
The initiative of a player taskgroup is determined by ...the ranking officer, i think. I believe AI NPRs use preset initiatives depending on their race. If your beam ships are out-initiatived, the only way to keep the range closer than the enemy ship's speed is to split up and use flanking/encirclement tactics.