I suggest you show it to a doctor or dentists skilled in the diagnosis of the inside of the mouth. A dentist would do. This does not sound like herpes or an STD. Herpes typically affects the outside of the mouth, near the lips, not the inside. Also, it doesn't come and go every couple of days and last a day. I advise you not to play with or rub it, and get examined by someone whose opinion you will trust.
Take care.
Dr. Rockoff