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Collaborative problem-solving (CPS) in STEM+C education involves cognitive coordination and emotional regulation during joint tasks. Prior research has examined discrete affective states in learning environments but less is known about how these emotions evolve over time and affect CPS behavior. This study investigates the temporal dynamics of five emotions—engagement, confusion, boredom, delight, and frustration—using Markov Chain analysis of data from high school pairs building computational models in the C2STEM environment. Emotional transitions aligned with cognitive processes, seen in interaction patterns like PLAY, ADJUST, and BUILD, to analyze affect during modeling. Results show that emotional trajectories closely relate to cognitive actions, including construction, simulation testing, and debugging. Transitions that maintained engagement linked to productive collaboration and stronger performance, while ongoing frustration and boredom indicated disengagement progress.