[Alan Anderson]

Running Robot Main will copy all the necessary VIs to the cRIO's RAM and execute everything there. It does not save anything to the cRIO's flash memory, so the next time the cRIO boots up it will run whatever it had stored previously. It's useful for testing and tweaking and debugging, but it doesn't survive a reboot.

Choosing Build compiles all the project's VIs into a real-time executable file that the cRIO knows how to run. It doesn't put that file anywhere on the cRIO, though. You can do it even if your cRIO isn't connected.

Choosing Deploy copies into the cRIO's flash memory whatever real-time executable file was most recently built. It doesn't explicitly set that file to be run when the cRIO boots up, but if you've imaged the cRIO with the "always run deployed code" option set the file will be run anyway.

Choosing Run as startup copies the real-time executable file to the cRIO's flash memory and sets things up so that the file will be run when the cRIO boots up.

There's no good reason to use Deploy. Get in the habit of always doing Build followed by Run as startup when you want to put a program on the cRIO.