If you have download a program using the Xamarin Add-in the Firmware application will be terminated. This is done to prevent two applications from writing to the LCD and listing for button events. If you have uploaded a program the only way to start the firmware application again is to restart the EV3. I will update the Xamarin Add-in page about this information strait away. I am currently working on a button in the Add-in that lets you restart the firmware application.
PS: The very first release of the Add-In (only downloaded by 2-4 persons) did not show the MonoBrick Logo when uploading a program – this was very confusing as it indicated that the firmware was still running. If this is the case please download the latest Add-in.
A better way to turn of the EV3 unit when its in remote debugging mode is to connect via ssh and send command to turn of.
In OS X just use terminal, and for Windows you can download Putty and set up an ssh connection. Then send command:
“shutdown -h now” and the unit will shutdown like it does when shutting down from menu.