s10sleeper,
Metatarsalgia is usually defined as pain on the plantar surface of the foot, directly under the metatarsal heads. This is usually considered the ball of the foot, under the lesser toes. Metatarsalgia in the great toe is usually sesamoiditis.
If you have a loss of the longitudinal arch and it is not being supported with arch supports, it can transfer weight in the forefoot abnormally. As such you may be developing problems in the MTPJ's (metatarsalphalangeal joints) of the lesser toes.
This can also lead to osteoarthritis in the joints, as this is a wear and tear disorder, not an inflammatory one (as in gout). The only way to know if there is significant OA, you would need to have x-rays of the feet.
If the metatarsalgia pads and longitudinal arch support are not taking care of your problem, you may need to see a specialist in disorders of the foot, such as an orthopedic foot and ankle surgeon (an MD or DO) or a podiatrist (a DPM, doctor of podiatric medicine).
Unfortunately, this type of foot problems can become chronic in nature and very difficult to treat. Besides the inserts, you should always wear shoes with good arch supports, heel counters, and cushioning. Maintaining your BMI and weight also help with foot problems.
Hope you can find a solution to your problems. Good luck.