I hope the change fixes the problem.
These NPR fleets aren't using jump engines - its a stabilised jump point.
I had no idea they worked differently so I learned something today.
There are two mutually hostile non-combat NPR fleets on the same jump point. They both try to escape the other by transiting the jump point, at which point they find themselves in the exact same situation - repeat ad nauseam.
Unless jump shock was identical for both fleets, one would transit before the other and break the cycle.
For this specific example, at some point the NPRs should realise that the ships are non-combat and they can safely ignore each other.
Alternatively you could simply put in some logic that tracks how many jumps the fleet has attempted in the past 30 seconds, and if it reaches 6 (ie it has tried to jump every increment) then give it a 33% chance of waiting 1 increment and a 33% chance of waiting 2 increments before choosing the next action. That is likely to break the deadlock because they are unlikely to choose the same delay time, and if they do the situation will cycle back and try to resolve again.
They are non-combat fleets but they include combat ships (salvage ship plus escorts for example) so both sides are correct to attempt escape.
Also, it wouldn't make logical sense for an NPR to deliberately delay escaping a threat.
The fact that the fleets include combat ships does make it less clear cut.
But if they keep jumping away from each other it seems reasonable for one side or another to realise that neither side wants to engage and change behaviour. If one side wanted to engage, they would stay and try to lock weapons, and follow next increment to regain targets. By jumping at the same time they are trying to escape.
I think it would make sense for a commander, realising that neither side wants to engage, would be willing to retreat in a way that temporarily takes the fleet closer to the enemy.
Alternatively you could justify it as a small realism sacrifice for squashing an annoying gameplay outcome.
Maybe a different question to ask is why one both sides don't try to retreat in-system?
Rather than trying to flee to an adjacent system, why don't they attempt to link up with a friendly fleet or flee towards a core system?
As long as the path to a friendly fleet or core system is in a direction for both sides, it will cause them to break contact.