spatula I tried your suggestion of waiting a few seconds. That does work. I didn't realize the arduino reset every time a serial connection is made. Is this constant across the arduino line? Also has me wondering if there is a way to prevent the reset on opening the port. At the moment the most immediate solution that comes to mind is writing a daemon to handle serial comm with the controller.
Your thought on my not handling the \r \n characters. Technically I do handle any characters that I am not interested in. Those just get overwritten with the next character from the serial stream. Which probably isn't overly elegant but does make the code simple.
Thank you for your help. I will have to follow up with some daemon or other code once I have something working.