There are a number of things to explore here. First, is it only after you ejaculate? If you were to have sex for a similar period of time but not ejaculate, would she still feel this sensation? Is she sufficiently lubricated during penetration? If not, she could feel raw afterward. She would feel similarly if she is menopausal or peri-menopausal and having hormonal changes. Also what part of her vagina is experiencing the burning? Is it deep inside or is it more on the outside? If she is on hormonal birth control, she could be experiencing burning from decreased free testosterone levels. This would be felt primarily on the outer opening of the vagina. Sometimes some women are very sensitive to yeast so that even a small growth causes a burning sensation. In that case, it would be recommended that she limit her intake of bread, alcohol, and sugar during each meal so that she only has a small amount at a time. There are Gyn specializing in vaginal pain, which she may look into.

While her gynecologist says she is fine, and that there's no problem with your semen, it could be the combination that can cause the burning sensation. I wonder if the doc checked her right after you've had sex to notice the irritation or if it was days later. As, a good number of women are allergic to their partner's semen and it's helpful to check shortly after the initial reaction happens.

The other possibility is that she's rubbed a bit raw--so to speak--from sex, and your semen is further irritating her delicate vaginal tissue. Next time you have sex, try using lube during intercourse to see if it makes a difference. If it doesn't, try using condoms to decipher if it's an actual allergy. Just avoid using condoms lubricated with N-9, as that can be irritating too.

Do look at Amy and Madeleine's responses above. And go to your GYN! That's what she's there for!