Hi AK,Stress could cause that. If you have been under stress for a long time, you could get adrenal fatigue which can result in low cortisol levels. What are your stress levels? This could be especially true because you've had this happen before.
How are you sleeping? I had a lot of problems with my joints, especially my feet, after my oldest was born. They even tested me for arthritis. It was lack of sleep. To this day, if I sleep less than seven hours my feet bother me. Of course, stress levels effect how we sleep.
You mentioned food allergies, that would be my third idea.
There are some supplements you could try, MSM, glucosamine-chondroitin, chelated magnesium, high potency fish oil, maybe even l-glutamine if it is something in the muscles.
How are your stress/sleep levels? Keep in mind not just emotional stress but physical stress, too, like over exercising, illness, surgery , etc.