You probably need to CLEAR the PLC and write the entire project.
We think bad comm can cause this. Updating a PLC project or updating firmware with slightly questionable comm causes these issues. ALL OF IT must work. If one part (System Configuration, Documentation, Program) gets messed up - your PLC won't work right.
I would recommend ALWAYS doing a PROGRAM mode update - never RUNTIME EDIT when you have slightly questionable comm (large timeouts and retries can only do so much). If it works, then put the PLC in RUN mode. If it fails, try again. Keep trying. If it fails like what you are seeing now, you will need to CLEAR the PLC.