1. The property node in your init VI is not needed. Those properties are set in the Configure Serial Port VI.
2. There is no need to constantly set the file position to the end. You only need to do that once when you open/create the file, not before every write.
3. You should NOT have a wait in the file I/O loop. The queue data coming in will limit the loop rate. Otherwise, you need that loop to go as fast as possible.
What are you using for serial ports? If they are USB-Serial adapters, you need to check your device's power settings to make sure Windows doesn't just turn off the USB hub as a "power saving" feature.
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