Well I am not expert but I am going to have to say that perhaps it can be due to lack of support! I mean if you are running and wearing boxers rather then something a bit more snuggle to offer more support, then it may be the cause of it.
TBH, I would try to use a pair of more snugly under garments for running & see if there is any change...if not I would schedule an appointment for a mere check up for your situation.
Hope you feel better!
I dont know, because im a girl. Haha. but i agree ^ ditch the boxers for some tighty-whities. or go get checked out. no one on here can tell you for sure
you must wear a fit panty to support them .. when they sag they hit the side of thies .. next time wear good fit underwear ...