This paper presents results from an empirical study conducted with a novel subliminal teaching technique aimed at enhancing learners performance in an ITS. We replicated previous findings with the same technique but in a 2D environment. Non intrusive physiological sensors were used to record affective and cerebral responses. A brain analysis technique called Event-Related Potential (ERP), known to describe and confirm cognitive functions in the brain, provided strong evidence that subliminal cues and miscues were cognitively processed even though reported as not seen. The obtained results showed that only subliminal cues, not miscues, could significantly increase learner performance and intuition in a logic-based problem solving task.