If I had to guess, I would say it might be related to the musculature of the pelvic floor. Much of these muscles are stretched during pregnancy, and we don't think of re-strengthening them afterwards. Hence, when we resume activity, the muscular support in that area is lacking. Try doing exercises to strengthen your transverse abdominis for starters. This is one of your abdominal muscles, its fibers run across your "tummy", so picture it as acting like a type of corset for your organs. To strengthen it, you could begin by lying flat on your back with your knees bent (feet flat on the ground, like the position you would take to do regular crunches)....then try and suck in your belly-button like you were trying to touch it to your spine..navel-to-spine. The best way I can describe how this feels, and the simplest way, is that it's what you would do if your were urinating and contracted your muscles to stop the flow. There's your transverse abdominis working. Try this and when you have gotten accustomed to the exercise, I will gladly give you a progression to further overload this muscle. Hope this will help
Let me know. BTW, I don't guess you will see immediate results, give the muscle time to gain some strength. I would maybe subsitute your running for another lower impact aerobic activity for the time being.
Good luck!
P.S.: Make sure you are actually thinking about the "stopping the flow of urine" thing...otherwise, you will simply fill up your lungs with air, and this will give the result of your belly-button sinking, but won't be a contraction of the TA.
Hint: even after you have filled your lungs with air, you will still be able to perform further navel-to-spine...(through CONTRACTION)....
Sorry for the long post