Painful down there!

Me and my so have been intimate for about 1 year and 3 months. I'm on depo, so we choose not to use condoms. The past three months everytime we've had sex, right when he *yaknow*, it hurts down there like crazy! Figured it could be a uti, so I went to my doctors and she prescribed me amoxicillin for 3 days. After I finished the meds, we tried again. Same thing happened. I don't know what it could be. Is it possible to develop a semen allergy? Or could it be someone more serious.