This paper introduces the application of formal modelling to cyber-physical systems for the purpose of formal verification of cyber-physical agnosticism properties of decentralised automation software. Service-oriented cyberphysical systems are modelled using the IEC 61499 function block architecture. Then, the IEC 61499 model is represented in terms of SMV formal language, which is verified using the nuXmv model checker. The timestamped events mechanism is implemented in IEC 61499 using the existing syntax of the standard. The impact of jitter on the behaviour of physical system is demonstrated in both simulation within IEC 61499 execution environment and in counter-examples extracted from nuXmv. The methodology presented in this paper creates the premise for automatic verification of the cyber-physical agnosticism of systems.