To prove something is running I set the pin 13 (LED_BUILTIN) to HIGH. The built-in LED on the Mega board does not light up. (It does for the Nano.) I also put a probe on pin 13 and it shows 0 V for the Mega. (Shows 5 V for the Nano.)
I put a probe on the 5V pin and yes, it does show 5 V so something is working.
I also tried to debug my sketch. It single steps through the code in setup() without problem but without any change to pin 13 or the built-in LED.
Another strange thing is that the debugger fails on delay() and jumps to the start of the setup() function.
I am running SimulIDE 0.4.14-SR4
Thanks for help.