I see two possibilities, assuming the investigations done have cleared a bony cause.
The most obvious one is along with the inversion MOI some trauma was sustained to the peronius brevis tendon itself. It could have sustained a partial tear that has not fully healed yet. You mention X-rays and bone scan, but has there been any attempt to do an ultrasound scan of the area (I don't know how easy this would be to get a viable picture as the area is relatively small). AnMRI would clarify this possibility further, although I suspect their symptoms are not of the severity to warrant that referral at this time. Alternately, I have seen people who subsequent to an ankle inversion sprain have developed a tendonitis/symptomatic tendonosis in the peroneii. I suspect this is due to overuse of these muscles while compensating for the ligamentous laxity. Typically this has presented posterior to the lateral malleolus, but I can't see any reason why it couldn't happen at the tendon's insertion.
I think both possibilities would be managed similarly. Settle down the inflammatory process, ensure the foot mechanics are good (or well supported) and re-build the strength/control when less irritable.
The other possibility, along the lines of your "nerve" theory, would be some minor trauma to the sural or lateral plantar nerve. This could easily have happenned with the initial inversion MOI, although I suspect the symptoms would be a little more diffuse than they are described. You will need to do some specific neurodynamic testing for this to rule in/rule out certain peripheral nerves. If you are unsure about how to do this, consult with a colleague that is a musculoskeletal/manual specialization, or someone who has taken at list one the the NOI Group's nervous system courses. Remember that you can get some false positives with neurodynamic testing if you don't take into account that you are also stressing other soft tissue (tendon, ligament, etc.) structures with the various positions. You need to do it all, write down the details as you go, then put it all together in the end. Good luck!