This behavior started, I think when the Debian Jessie distribution appeared.
Prior to that, the PRUs started up at boot perfectly as far as I could tell.

Later, post-Jessie, I worked around it with similar methods to what you are 
doing.
I didn't consider it a serious problem since I could start up with either 
.profile or .bashrc.  
My projects are hobby/learning so not for serious embedded deployment.  It 
would be good to understand what is going on!

You can also try this:

echo "4a334000.pru0" > /sys/bus/platform/drivers/pru-rproc/bind
echo "4a338000.pru1" > /sys/bus/platform/drivers/pru-rproc/bind

and this

echo "4a334000.pru0" > /sys/bus/platform/drivers/pru-rproc/unbind
echo "4a338000.pru1"  > /sys/bus/platform/drivers/pru-rproc/unbind

If the above commands work, this might provide an additional clue as to 
what is going on at boot.

I'm hoping to get back on another PRU project soon, would be nice to get 
this mystery resolved!

Regards,
Greg

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