Thanks Pierre.
Sorry guys, I discovered I pulled a real blunder here
I discovered that I had only been using the STOP command instead of ESTOP in my inputio.fil. This has been the case for the last 23 backups of my file, and before that, it was cnc lite.
There may have been some reason why I used only the STOP command then, but I've forgotten what it was now.
Without the ESTOP command being read, the contents of Estop.fil never gets read!
So, with that fixed, there is far less trouble. The STOP command would of course, have stopped all the motors, but not the program in sequence. This resulted in the Galil error coming back through because it could not execute with the motors stopped.
Now, after Estop, there are no annoying messages, however the motors are still off, even when the Estop button is released. At this point, I have added an operator message to hit the Escape key. As soon as the shutdown dialog comes up, the motors turn back on, and I can cancel out of the shutdown.
The machine remembers it position, so after a simple return to home position (not the homing routine), I am up and running again.