Arduino locks up, powering down doesn't fix but serial monitor does

DrAzzy:
I suspect your chip is being backpowered by one of the connected devices, so when you power it down it's still running.

I don't think so - Nothing connected is powered - boiler on/off just senses light from an LED, zone on/off are just contacts that close....... All LEDs on the board go off when power is removed.

Thanks for the comment