Podiatry is good.
You hold shoes and flip-flops on to your feet differently. it may be that you have been using differnt sets of muscles and a lack of support and cushioning from flip-flops may have resulted in strains that you would not get from shoes. This may resolve after a few weeks without any treatment.
You will need to be quite specific with your GP. I have pain in the ball of my foot after an accident a couple of years ago. It's symptoms are similar to a condition known as Morton's Neuroma and this was what my GP wanted investigated, rather than asking why I had pain. The consultant advised that I didn't have a Morton's Neuroma rather than finding out why I had pain.