If you had a positive swab from the genitals, you have genital herpes. The swab test takes a sample from genital sores, so what you have is genital.
Could you also have an oral infection? Yes. However, oral and/or genital herpes doesn't cause continuous symptoms for 6 months.
Perhaps it's an allergy. It could be your toothpaste, mouthwash, a food, a beverage, smoking, etc. If you are using a mouthwash, stop using that first for like a week or so, see if there is any improvement. If not, try changing toothpastes. Continue that and see if you can figure it out, and schedule an appointment with a dentist. They can often figure out things of the mouth when doctors can't.