wsnook thank you.
The Arduino as setup in a black box that only can be seen through the PI. I hooked up serial1 that output to uart serial to USB converter so we could see on a monitor what the arduino was doing by putting in message in the code. Very helpful for trouble shooting and understanding what was happening.
We wanted to the Arduino code to be stuck in a loop so we could look at IO directly. But when we did that after about 8 -10 second in loop the Arduino was forced into a reset.
I had not realized the opening a serial port reset the arduino, great find. I guess that was obvious because when you use the Arduino monitor it does reset the arduino. Thank you so much for the reference.