Trials of lysine for herpes treatment have, by and large, shown inconsistent results. There are questions about whether or not supplementation works at all, and even those studies that have shown a positive effect have led to no standard recommended dose. That having been said, however, there is a theoretical mechanism by which lysine could conceivably work to treat herpes.
In some laboratory studies, lysine has been shown to inhibit the activity of arginine - another amino acid that tends to promote the growth of the herpes virus. If the relative amounts of lysine and arginine in the body do affect herpes symptoms, then it is understandable why it would be hard to do a study that shows the efficacy of lysine supplementation. People get varying amounts of lysine and arginine in their diets, and it would be extremely difficult to modulate their relative amounts via simple supplementation.
There isn't enough data to make me comfortable recommending lysine as a herpes treatment, particularly as compared to more traditional suppressive therapies, but if you're taking it and it's working for you then there's no reason to stop. If you're following the directions on the package, lysine is unlikely to harm you, and it may even help. Just because doctors and scientists don't have enough conclusive evidence to make a general recommendation about lysine doesn't mean it might not be a good adjunct herpes treatment in some people.
Robb-Nicholson C. (2007)"By the way, doctor. For years, I was plagued by cold sores and took antiviral drugs to treat the outbreaks. But at a friend's suggestion, I started taking lysine every day, and it seems to prevent them altogether. What do you know about this supplement?" Harv Womens Health Watch. 14(7):8.
Perfect MM, Bourne N, Ebel C, Rosenthal SL. (2005) "Use of complementary and alternative medicine for the treatment of genital herpes." Herpes. 12(2):38-41. Review.