[airnate]

The first thing that I notice is that you are using Controls to specify which channels you are using. You should right click these and Change to Constant because otherwise they will revert to the default value of the control when you deploy a stand alone executable and reboot.

Other than that I don't see functional problems with the code.

Aesthetically you should separate your subVIs on the diagram so it's clear where the wires are going. You want to expose all the wires and try not to cover any of the wires up when possible.

Are you still having functional difficulties?