Diagnoses recorded on the problem list are increasingly being used for decision support applications. To obtain insight in the adequacy of the clinical user interface to capture what the clinician has in mind, and to reconstruct the clinical reality of the patient, we analyzed in the database of an EHR system the transactions that resulted from managing the problem list. Our findings indicate (1) that caution is required when using the evolution of the problem list for determining comorbidity or ongoing disease, and (2) that similarities or differences in problem list annotation sequences do not always correspond with similarities resp. differences in disease courses. It is to be investigated whether automatically identifiable subsets of problem list evolution patterns exist from which ground truth reliably can be inferred or whether clinicians need more education in how problem list user interfaces should be used to avoid erroneous interpretations by clinical decision support applications.