The literature consistently reports that students express some degree of discomfort when they are thrown into self-directed learning environments. In this paper, we present the preliminary results of an investigation of the causes of student discomfort in several different self-directed project-based courses. Our results suggest that student motivation and opportunities for the development of deep understanding and transferable skills are important in creating a positive self-directed learning experience. Negative experiences and student discomfort in self-directed environments may stem from problems with self-regulation, low self-perceptions of content learning, lack of personal engagement with the topic, and difficulties related to the social learning environment.