What is the logic for the NPR jumping back and forth through the same JP? Perhaps fixing that loophole will resolve this issue.
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.
I agree that in this particular case, adding a random jump shock will break the cycle. Although in the cases mentioned by others, jump shock doesn't really fix the real issue.
Maybe for the NPR, instead of making decisions using "if A then do B" logic, some randomness can be added into the decision-making, like "if A then x% do B, y% do C, ...". The list of options and the weight of each option can be determined by say the race's properties, or the battlefield conditions (such as friend-foe force ratio, or known intel about the ships insight). This way, the NPRs will not always make the same decision in the same situation. In this particular example, if one NPR knows the other NPR's ships are non-combat, it may decide no need to escape, or the NPR with a 'larger' fleet may decide not to escape.