First guess: timing issue. Especially since you said it works in highlight mode. Specifically, when you are not running in highlight mode you're probably not waiting long enough before trying to read, and the loop immediately detects no bytes on the serial port. That delay function in there will not guarantee a 1 second delay between write and read . There is no data dependency - a rookie mistake. Either use a sequence frame or use the Time Delay VI to have error clusters to wire through to establish data dependency.
