Industrial automation is a complex process involving various stakeholders. The international standard IEC 61499 helps to specify distributed automation using a generic architectural model, targeting the technical development of the automation. However, analysing the correctness of IEC 61499 models remains challenging because of their informal semantics and distributed logic. We introduce new verification techniques for IEC 61499 applications that combine a design-time analysis for computing a formal model of the application with a runtime analysis for extracting additional information during the execution. This combination of analyses allows for building a richer model of the application and thus formally verifying it using probabilistic model checking. Our approach is automated using several tools and was validated on a realistic IEC 61499 application.