@Douglas-Kryder @ccs-hello One more point. I've not yet metered the O2+ in the troubled dock configuration. Have only "known" lack of power up by lack of LED, basically not knowing all of the facts. Just got out a USB-LVTTL converter. Will connect later today to tty0 in breadboard dock to see if I can reflash. If so, the O2+ device may emerge from some hosed up state that prevents full boot, or perhaps even continuation past very early boot, to come up in a healthy state that will work in all configs. --Bill

@György-Farkas Thanks again for replying! About the 3 seconds... it is desired and acceptable, having to hold the momentary switch down for 3 seconds to turn on/off the device ensures that it is not turned on or off accidentally. (This project is being run from a battery) I'm just a little annoyed that it takes LONGER than 3 seconds (10-13) to boot up the MCU. I agree your suggestions would work, but I would like to avoid having to make hardware changes to the board... in case this project happens to be manufactured in any considerable number. (The arduino dock is mounted on a pcb, so I was kind of hoping there would be a hardware fix that I could make to MY pcb to fix this... without resorting to altering the Arduino Dock board) I wonder if anything could be done in the Omegas boot code to pull pin 19 low sooner in the boot sequence or if is something that can't be avoided due to the Omegas internals.

@György-Farkas Well I have tried pull down resistors, but the problem is that those pins aren't floating from the beginning, as probably the internal multiplexer does something before loading the kernel. As shown on logic analyser graph pins actually go high for around 7 sec and have 1us pulses every 25us or so, which are then detected by 74hc595. DPIO 11 doesn't have those pulses, but stays high (output state) till you don't run a scriptwhere you set the output to low on other side others - 17, 16, 15 go to floating state after that. I then decided I will go with i2c port expander for more safe and predictable operation. MCP23008 is quiet handy as they are used in relay dock and have libraries written for it.

@Fabian-Nydegger-0 So this used to work verbatim. the second ampersand is b/c the python script never returns so i would like to Omega LED to stop flashing and finish the boot sequence. Also, the device is used as an AVR Programmer using AVR dude (from the arduino dock 2 package with a modified avrdude config file), so the device shouldn't be powered on longer than a single day. I could possibly remove the ampersand from the setup line. I removed the setup shell and replaced it with the gpiomux commands directly and that seem to correct my issues also the python pyGPIO module has a bug in it that I can't spend time trying to address ATM. So i just worked around it.

@Chris-Stratton thanks for your feedback. Until such time as Onion change their stance on powering off their device or one of my Omega's fails I will reboot with the procedure I am currently using.