Thanks for the feedback. The "click-to-focus" happens on the Window manager level, not application level. Not entirely sure if that possible with Mate, but I'll see. I'm already working on other improvements like the mount/dome/cap panel..etc so it will take some time.

Here are the steps to reset and get the Arduino seen by the computer again. I'm not sure why it dropped off, but it nearly appeared to be dead (at least on the connecting side).
- Tools --> Port (grayed out, or may show a different tty*** port and doesn't name the Arduino)
If using Windows it will say (com [number] - and won't list the Arduino name next to it)
- Have a firmware ready to compile and load. (I had 1.1 ready and just re-installed it)
- Hold down the reset button on the corner of the Ardiuno
- Click the "upload" button on the Arduino IDE software.
- When it says the upload has started, release the reset button.
- Moments later it will say "upload complete", no errors, and you'll see the Arduino is listed again under Tools --> Ports.
Done!
I think I'll probably have a spare Arduino arriving tomorrow, rather than a replacement which I thought I was doing since I thought something blew up on the one that quit.

Tom