I'm not a doctor (just a runner) but there are too many scenarios that could be factoring in. My top three guesses, would be the following:
1) Get a lot of rest.
It's surprising how long some seemingly basic injuries take. I'm still working through an ankle roll from two years ago, a tailbone injury took years... it's tough and often very frustrating but you need to be patient.
2) Proper Shoes
If you're flat footed you may need more supportive shoes. Hit a well-respected running store to have your foot and gate reviewed. Something like flat feet could lead to over pronate causing your leg to twist which may be impacting the injury. It may not show up during your run due to adrenaline covering any potential pain signals.
3) It may not be fully healed
Seriously. A close running buddy of mine is currently recovering from surgery from an injury ~15 years ago. He has been effectively running on a broken foot the entire time but it took a while to really impact him painfully. "Funny" part is that he eventually went to a doctor not for foot pain but because he was experiencing so much knee and hip pain.
In short: It may be an easy fix but hard to diagnose online.