When the runtime is updated, it may happen that after the process station starts, the platform type is misdetected (as IPLC201/301 rather than MXPLC). The result is wrong assignment of communication ports and other interfaces. It is easily recognizable, as the MXPLC does not beep twice after restart, and communication with COM ports as well as with the internal I/O module is not working properly. In the Converter mode, the internal I/O module is not detectable, nor the external I/O modules at the COM ports.
The problem can be easily fixed in Platform Config. Select the PLC, and click Advanced Servicing. There is Platform detection mode selector in the dialogue. Select the correct option, i.e. ForceMXPLC for a MXPLC process station, and click the Set button. This will force the MXPLC platform type. After restart, the process station should be initialized correctly: it beeps twice shortly. (In the Converter mode, there are three long beeps).
Use the IDE version 19.8.2014 available here.