Yes herpes outbreaks will clear up on their own. The time to re-occurence differs with everyone. What you descibe does sound like "slit type herpes".
Are they sore when visible? If yes, get re-tested, you may have gotten a false negative. ( which is much more common than a false positive). If they aren't sore, is your labia generally dry? If so, than it may be you just need to moisturuze it daily with ky or one of the other vaginal creams.