Sounds like you have a Morton's Neuroma, a condition that affects one of the nerves that run between the metatarsal bones in the foot. Symptoms include pain, burning, numbness and tingling between two of the toes of the foot. I've had one for about 6 years and you just have to manage the problem. As soon as I stop exercising the pain subsides and you wouldn't know there was a problem. It comes on after around 20-30 mins.
I manage mine by reducing any restriction in my footwear, socks etc. I've pretty much tried everything but found that wide fitting trainers and very loose sock or bare feet is the best way. Some makes of trainers such as New Balance just don't suit and agravate almost immediately.
In extreme circumstances you can have invasive surgery to remove the offending nerve but that's not for me.
Google Morton's Neuroma for details.
HTH