I think I misunderstood that the Read/Write Control (FPGA interface) was a property node. I think I see now that you are refering to the control/indicator values on the front panel of the RT vi.
I am quite happy to eliminate the value property nodes altogether and just have a blank front panel as these are just for test/clarification purposes to see if the block diagrams were working correctly.
What is important is the values from the Read/Write Controls being processed through to the VISA serial output and not the front panel.
Your RT code is fine, just put the all of your configuration and closing code on the outside of the loop. This includes the Open Serial port and Close serial port, Open FPGA reference and Close FPGA reference. You don't want to be doing all of that reconfiguration at 1kHz.
My stand application works perfectly now. Moving both the Opening and Closing of the Serial Port and FPGA reference outside the loop in the RT vi has solved it.
PW_nz, Are you still using the value property node on your RT Side? Or you never used it. Cause others have experienced problems using it on the RT side and removing solves the problem on the stand alone application.
I'd like to know to better help others in the future
As StevenA wrote I have no value property node in my RT vi. If you look at the zip file "Wheelchair Stability Control2" you can see how it has been set up.
Also as StevenA had suggested I moved the opening and closing of the Serial port and FPGA intereface reference outside my while loop and that has solved the problem completely. Annoyingly simple really.