Genital Warts?

I have a rather large sore on my vulva, however it only causes me discomfort during sex. The sore is flat and very dark almost purple usually, however on the last breakout when it was going away it looked skin colored and not purple or irritated. I went to my doctor and was told that i have genital warts(she saw other warts) and that she thinkgs i also have herpes because of the fact that these sore disappear and reappear in such short amounts of time, and the large one appears always in the same spot.
I don't believe that i have herpes because the sores only bother me during sex and from what i have heard herpes hurts all the time and you can feel them coming on, which i can't.
Can genital warts appear and disappear over short periods of time?