Three questions:
How long have you been running (as a regular form of exercise)?
How long have you been using orthotics?
When was the last stress fracture, and was it related to running?
These are important questions to answer before settling on any strategy for recovery, including calcium supplementation. Chances are, there is something about your anatomical structure, conditioning, or running style that predisposes you to stress fractures. In other words, your bones may be plenty strong enough, but over-stressed at one point or another due to factors you may be able to control. A prescribed orthotic is usually a clue that your foot-plant is not "normal" without it. The danger there is that an orthotic may redistribute pressure among the bones of the foot in a way that produces too much pressure on a particular bone or joint, at least when running. Impact sports like running routinely triple the pressure on the bones of your foot during each foot-strike, and sports docs create special orthotics to handle this pressure. Nothing against your podiatrist, but it is possible the orthotic you are using is focusing pressure on the 3rd metatarsal, or that it pitches your weight in that direction, at least when running.
I wish I knew what condition led to your prescription for orthotics. Perhaps you were considered to be an over-pronator, with what is generally referred to as fallen arches, or "flat feet." Maybe one leg is effectively longer than the other, which is very common condition that can often be corrected without surgery or orthotics.
In case it does turn out that your bones are considered fragile, there are many factors involved in the production and maintenance of strong bones than calcium. One reason I asked how long you had been running, is that gradual and regular pressure applied to bone tends to toughen and mineralize bone. The danger of prescribing exercise for loss in bone density, of course, is too much too soon. If you were told to exercise and plunged into the sport too quickly, stress fractures might be expected.
The other possibility, which is mineral deficiency, can be complicated to solve. Regular direct skin exposure to direct sunlight in temperate latitudes during the warmer seasons for about 20 minutes a day has been shown to stimulate enough vitamin D production to enhance calcium absorption in the body. Ingestion of vitamin K2 (a product of fermentation) has been shown to insure the proper distribution of absorbed calcium, into bone where it belongs, as opposed to arterial walls, stones, or bone spurs. The other minerals that make up bone have to be in there as well to form a healthy bone matrix, which also relies heavily on collagen production. One of the most frequently neglected minerals is Magnesium, which is hard to absorb, and should represent about half of your calcium intake. Underpinning all of this is a healthy digestive system, without which you will have trouble absorbing the above. Lots to talk about on that subject alone.
I'm worried about your history with stress fracture, stress reaction, and orthotics. Sounds like a perfect storm for further injury if you are not careful. IF you feel up to it at the moment, it might be a good time to have your gait analyzed on a treadmill by a physical therapist, with and without the orthotics, to see where the initial stress may be coming from, so you can develop a comprehensive plan to insure safe exercise and running in the future.