I had problems with those pins and found that the resistive "loading" at 
boot needs to be quite high.
I did not get this at first, and I had a bipolar transistor switch 
connected which was something on the order of 50kohms input resistance.
Well, that was too low for reliable boot process!  Sometimes it would work, 
sometimes not.  Very confusing until I found the special function of those 
pins.

Another example I had is the PRU cape.  It uses those pins, but the circuit 
attached is MOSFET input gates which are extremely high input resistance.
With this sort of circuit, the boot process is unaffected.  So it can be 
done, just be aware of the circuit you are attaching.

Since none of my projects require more than a few GPIOs, I simply avoid 
using the pins which can impact boot.
That's one nice thing about Beaglebone, it has a lot of GPIOs!

Regards,
Greg

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