I've been testing more... It seems that in order for the new firmware to be loaded to the node and then show as running in MyController the node needs a hard reset (pull power and restore). Issuing reboots from the controller does not seem to work.
I've yet to figure out what combination of things is actually triggering the update though. I just keep trying different things and eventually it works. But consistently the new firmware version will not be shown in MyController until a hard reset on the node is completed.
I'm using 5v 16Mhz Pro Mini.
I've also noticed that once the firmware version has been put on a node I can't re-send the same version, I need to increment the versions everywhere. Is this correct or should I be able to re-flash with the same firmware version by issuing the command?