Assuming that the transits are all strictly less than 4 hours…, I agree with
@djkelly69 that it may well be a mileage problem.
Great Circle Mapper shows you within 40 miles of the max allowed, but the problem is that QF don’t use GCM to calculate the milage, they use something else (sorry, can’t remember what it is). Consequently there can be differences in the milage calculations of every sector. These differences can be positive or negative, and generally they are relatively small. But over a number of sectors they can accumulate, and when you are operating near the limit, can push you over the max.
If you call again, I suggest you ask the operator to go through the sector distances and compare with what you’re getting from GCM. Unfortunately, this will only confirm that your itinerary goes over max mileage- the QF distance is final, and the GCM distance is irrelevant to them (sad face). But at least you’ll know what the problem is for sure.