When I was in my thirties and I was running a lot, I used to get pretty intense cramping just like what you're describing--like menstrual cramps only more painful. They'd start maybe two miles or so into a tough run and sometimes be so bad I had to stop and walk for a while. The docs I saw never figured it out (maybe because they were men?), but then I read an article that suggested it was due to hormone secretions prompted by the exertion and I should try taking a low dose of ibuprofen before going out for a run. That solved the problem.

Now I don't run any more, but I haven't had that kind of cramping during exercise since I hit menopause.