Here is what I have got so far, first the wiring pi library needs to be updated. When I used “gpio readall” it returned that the model board could not be determined.
After updating gpio the read all command worked fine.
Next I ran through each line of the shutdowncheck.sh and now find that when the shutdown and the boot pins are programmed such as when they are written “in”, “out” or given a value, it does not actually have any effect on the pins themselves. However if I am in the terminal and program the pins directly using
gpio mode 25 out
gpio write 25 1
for example, then this has a direct affect. In my case I have put the boot pin on 25. Using the above commands turns on the boot light. But when the system starts, the boot light does not come on.
Next I will find out why, but you should start with updating the wiring pi library since likely yours is old