I'm no expert on the subject, but I get them now and then (the little bump on the inside of your cheek/lip, not the outside ones on skin). I have found that mine are mostly due to:
1) accidentally getting the wrong toothpaste - so good for you on that!
3) Eating a lot of acidic foods in a short period of time... like when tomatoes are newly in season and I go overboard.
Have you been stressed about anything lately? Eating anything more acidic than usual?
Just a couple thoughts. I really have no idea though.