I had a friend who was experiencing the same thing and it ended up being varicose vains. Her Dr suggested getting a belly band. I would mention it to your dr and see what they can suggest. :-)
It could be the way that baby is laying. As you get further, more pressure is put on it and it gets pretty uncomfortable.
I had this issue to. My doctor said it was just ligaments and muscles stretching. Laying down on your side and heat helped me :)
Research pelvic girdle pain... Could be that :)
I got that in my first trimester, but it's been coming back now in the third :-/
Also... You say "vagina".. But do you mean the labia area? Or groin area? Or pubic bone area?
If it is more internal, it could also be the baby pushing on your cervix from the inside....