Water runs periodically in my toilet?

Hello. I have replaced the entire inner workings of my toilet, but ocassionally the water will kick on and refill the tank. I've noticed when it does this that the water is just below the water level mark. I have adjusted the water lever that controls the amt of water in the tank and I have checked the flapper. However, it is still doing it about once every 2 -3 hours. The overflow pipe is not a problem either. What can I do?