Lots of things could be causing the problems, and there are a lot of things you could try. I think it is possible that the lubricant or latex are causing a bad reaction. Try a polyurethane condom and a different kind of lubricant and see if that makes a difference. How slowly do you two go when getting warmed up for sex? A more aroused woman has a vagina and cervix that are more prepared for sex, which means less pain. You could start by going down on her, mutual masturbation, or using a vibrator. It could also be that "in the moment" she is aroused enough that she doesn't feel uncomfortable even though her inner walls are being bruised, which she feels later.  Physically stretching the vagina before entering her with your penis could help with that. Spending a while fingering her, gradually inserting more fingers, could help the vagina to open up, as could using a small vibrator. Having an intermediate step between no insertion and a large penis could help the vagina adjust.