Some stds can cause sex to be painful.
I had the same problem you are explaining, after a full std panel, everything was negative and I was talking to my dr. The way he explained it to me. When a woman is aroused, her vagina swells a little bit, there is alot of blood flow to that area. If she doesn't orgasm, the swelling stays, which may be what is causing the discomfort (think of a guy with blue balls, Chicks get it too!) so you can either wait a few hours/a day or so to let it all go away, or just finish yourself off
I was still married then, so I went home and told my husband (now ex) my dr told me the reason it hurts after sex and I swell is because you aren't licking it enough! lol then I explained what he really said, and all I got was "Your dr is a douche" lol