The swabs are pretty conclusive, as long as you had the swabs done no more than about 48 hours after they first presented. These tests require the ability to collect enough material from the lesion to grow virus (culture) or detect DNA in (PCR). So it's possible to return a false negative on a culture.
So my suggestions are these: the very next time you have fresh symptoms, go and get another swab done. Make sure they do a PCR, which is more sensitive than a culture.
Also, get your doctor to order the Western Blot for you by calling the number on this page:
http://depts.washington.edu/herpes/faq.php#faqCat-4
It's the gold standard of HSV testing and 99% accurate. It will cost a little more and take a bit longer to return results, but it will be worth it. It will be conclusive.
Meanwhile, you might try some of the over the counter topicals for herpes. I've had some of our support group members swear by such topicals as Dermoplast, Aquaphor, Releev, and Abreva. Make sure you run these by your doctor first, however.
Good luck to you. Crossing my fingers that your discomfort resolves soon.