The problem with M05 and Stop at Tool Change sounds like a Regen Resistor problem, or the Regen Circuit on the Drive Power Supply (PSR) is Bad and needs repair.


Side-Note: If the RTCPU setting were lost you would have boot up problem more than just Spindle IO.
The WSCPU and RTCPU board assemblies have battery backed up and refreshed CMOS settings.
If you have the RTCPU with Dallas Clock-Chip the battery is internal to the chip and the chip must be changed. There is a hack to add a battery on top of the chip; but skill is required.
The WSCPU Bios can be reprogrammed with a keyboard as you show in your pictures using the settings documented in the A2100 Control Reference Manual using the Board ASSY# 3-424-xxxxAyy found on the board Chassis.
The RTCPU board settings were normally Flashed onto the board via a Cincinnati ESD Floppy disk program with the BIOS settings per the Board ASSY# 3-424-xxxxAyy found on the board Chassis.
If you provide the Board ASSY# 3-424-xxxxAyy found on the board Chassis to the "Forum"; maybe someone has documented what they were on a bench while they were correct.
Otherwise you would need to send the board to someone in a Cincinnati Technical Support Service group that can reprogram the board and test it for you.
The RTCPU Board talks to the A2100 Real-Time System: PLC-Program, I/O board, Servo Board, Handheld Pendant and converses with the WSCPU.
Software is loaded onto the RTCPU board at power on after diagnostics is run.
Also without it working properly you are crashing the windows NT hard drive when you power off unless you have disconnected the Hard Drive first!
Caution: This can corrupt a hard drive!