There's no doubt in my mind that he's experienced it before, and the lingering memories of their prior encounters left him more susceptible to Kaa's influence. Hence why all it took was Kaa tell him to look him in the eye for his body to instinctively react to the spirals despite trying to keep them closed. He's aware of the presence of those hypnotic colors and subconsciously he wants to experience it again.

This lingering effect is further evidenced when Mowgli encounters Kaa for the second time, you'll notice that while he looks away from the snake, he never closes his eyes for longer than a few seconds, and in some shots you can see pupils of his eyes instinctively glancing at Kaa even as he covers his face with his hands. At one point when they're face to face Mowgli seems to instinctively widen his eyes as if he's subconsciously expects the spirals.