I'm not a doctor, but I've had oral herpes my whole life and this is my opinion:
herpes doesn't usually happen on the inside of your mouth or on the middle of your lips. It sounds like ulcers (which is NOT contageous and NOT related to herpes) or just chapped lips, especially if its occurring one after another after another. Herpes doesn't occur more than once every month (or even less than that usually) and its impossible for herpes to flare up and disappear within a day or two. If its not herpes it makes sense that Lysine wouldn't do anything.
To be sure you could visit any general practicioner and have your lip swabbed for a herpes test.
Also, and again Im sure there are exceptions to this, but herpes generally occurs on the edge of your lips where it meets the skin, whether or not its on your bottom or top lip.
As a rule, it will also NEVER cross your mouths mid-line, but can occur ON the midline itself. If you have sores that jump from one side of your mouth to another, or stretch across the middle, herpes is most definitely not the cause.
Lysine doesn't do much for cold sores to begin with.
This sounds more like something non-herpes going on. You've had cold sores enough now to also recognize that this is different. Next time it's there, try to see your doctor or dentist that day and have it looked at.