Maybe running caused flare-ups because
1 you were overdoing it
2 you weren't warming up/cooling down properly
3 you had a stress fracture that never healed right
4 you actually have a 6th toe growing (don't laugh too hard, one of my sisters complained of foot problems for years, and finally after like 30 yrs of complaints, went to a doc, the doc feels the foot, goes "hmmm, let's get an X-ray", X-ray shows an extra "bone sprout" along the bones that make up the arch of the foot, doc says, "hey, your body looks like it is trying to grow an extra toe, let's get rid of it", surgery happens and with a bolt-cutter like tool, clips off the extra bone, and now she has a problem free foot...and yes, I occasionally rib her about being a mutant.
5 something else I can't think of in the moment...lost my train of thought with the story of my mutant sister
6 combo of the above.
Anyway, no matter, glad you got past it. For my own flare-ups, I just think I will need to not wear the tight shoes.....oh well, there goes my presentation tomorrow for the Board....maybe I can hide the comfy shoes behind a desk or something.