You've got some issues with your code.
First of all, in your subVI's, you have a most of your controls hidden on the front panel. This makes it hard to find the controls and determine what their default values are. You have them wired to the connector pane, but you never really wire anything to them where they are placed in your main VI.
Second, you have 4 single frame flat sequence structures in your main VI, but none of them have any control over the data flow. Three wrap around each subVI and a delay timer. The fourth just wraps up those 3. Those 3 frames of code are all going to execute at the same time more or less, and the two subVI's will execute right away. The Delay timer doesn't delay anything, but having the main VI come back to edit mode at the end of execution.
Third, both subVI's are set to write to com port 1. They also both close the com port. Since the two subVI's execute simulataneously, you'll actually have somewhat of a race condition of how the code inside them execute. A serial port is a single entity that can only transmit the data sent to it in series. The two VISA writes in the two subVI's will actually all compete with each other as to which one executes first. My guess is that the order of the writes are getting jumbled in a way that the device never gets the second message accurately.
