Education research has explored the role of students' affective states in learning, but some evidence suggests that existing models may not fully capture the meaning or frequency of how students transition between different states. In this study we examine the patterns of educationally-relevant affective states within the context of Betty's Brain, an open-ended, computer-based learning system used to teach complex scientific processes. We examine three types of affective transitions based on similarity with the theorized D'Mello and Graesser model, transition between two affective states, and the sustained instances of certain states. We correlate of the frequency of these patterns with learning outcomes and our findings suggest that boredom is a powerful indicator of students' knowledge, but not necessarily indicative of learning. We discuss our findings within the context of both research and theory on affect dynamics and the implications for pedagogical and system design.