I'm probably not going to directly answer your question here, but this has been my experience.
You're probably damaging your muscles and ligaments because you're not giving them proper recovery time, you're overdoing it, or you're not doing the proper build up when coming back from your injury. I seriously doubt the food you're eating is making a difference as long as you're getting adequate nutrition. Maybe you need to seek out a medical opinion. Oftentimes we can become asymptomatic, but the problem may not be fully resolved. Sometimes we work through pain until it becomes unbearable. I'm just as guilty as anyone else, maybe even moreso.
As someone who's dealt with chronic injury (the strain, restrain cycle) the thing I've learned is that the affected area needs to be restrengthened slowly and I need to be comfortable in what I'm doing before I move up a notch. In my case, it was my hip flexors which were being reinjured, recovered, then reinjured. You need to respect where your body is, and just because you're capable of doing something doesn't mean you should be doing it. My example for myself would be that I can fairly easily run 10 miles at a sub 8 minute pace, however that doesn't mean I need to be doing that. What I need to be doing is getting my body used to running 10 miles at a pace that is that is easy, conversational, and pain free. If I feel even the slightest twinge in my affected areas I know I should slow down. It isn't always easy because I feel sluggish when I'm running slow. I know however that when there is pain or twinginess during a run that my body is telling me "look, I've tolerated it this way for a long time, but enough's enough. Now it's time to meet halfway."