I also have had this problem. I never really thought of it as any medical problem, but I ended up here, because, I have never met anyone who knew what I was talking about and I wanted to know what it was.
It doesn't seem to cause any problems. I am sexually active, but I think the problem started before that (can't be sure). I have a tongue ring, but I also believe that I got it after this. I am 23 years old, female, and have no alergies to anything that I know of. Other than this mysterious, bothersome little thing, I'm overall very healthy.
Ever since I can remember, however, I've had this same thing occur on either side of the back of my mouth, above the jaw line, in that little nook between the teeth. It was hard to get to, but if you popped it, it would go away. When I started getting it under my tongue, I no longer got them in the back of my mouth anymore.
It also seems as though the more you pop them, the more frequently they reappear, but one can't really help but pop them, because they're so bothersome if you don't.