The second edition of the IEC 61499 standard aims to clarify the interpretation ambiguities of function block’s execution semantics. This resolves the pivotal issue of realizing portable and interoperable implementations of the IEC 61499 reference architecture. As the IEC 61499 standard is about entering its technology takeoff phase, these clarifications are timely and important. It is hence expected that more innovators of automation software tools, runtime environments, and control hardware will start adopting this technology. To assist such adoption, this paper presents a study of existing IEC 61499 tools’ portability issues. In particular, the features of currently active IEC 61499 tools, such as FBDK, ISaGRAF, 4DIAC, and nxtStudio are outlined. Their incompatibility issues due to different execution semantics are exemplified. Moreover, it is also illustrated in this paper how these issues can be addressed by complying with the updated norms.