This paper addresses formal validation of distributed logic controllers represented in Visual Flowchart Language (VFL) that is a high-level programming language used in industrial automation. Traditional validation approaches based on simulation become obsolete in reconfigurable manufacturing systems where complex machines have decentralized control and are built by reuse of components. The source code based validation is also important for OEMs to unify their development procedures from embedded systems to machine controllers. For modeling the VFL design we used net condition/event systems (NCES) - a modular formalism developed for modeling systems with distributed states such as closed-loop control systems in distributed mechatronic devices. The methodology was implemented in software tools automatically generating the model's modules given the controller's source code. Then the hierarchical NCES model is assembled into a place/transition net that is subjected to model checking. The proposed approach facilitates integration of formal validation into software/hardware development in control systems' engineering.