I've been playing a modded run recently involving heavy usage of pilums, and I've noticed something that appears to be consistent across most pilum-using ships with Fast Missile Racks.
When using a timid officer to stay at a very far distance from the enemy, the AI will launch their pilums as expected, activate their fast missile racks, and then launch the pilums again.
However, in this second launch, the AI will then vent the flux generated by the usage of fast missile racks mid-burst, causing them to only fire two of the three pilums that would normally get launched.
Speculation:
it may be caused by the AI's tendency to vent any flux they obtain when not near combat.
a possible fix may be causing them to not do this for very minor amounts of flux or adjusting the "must. vent. flux." behaviour when at extreme ranges.