Got past this one, the long and short of it (not in that order).
Pull the USB cord from the Raspberry Pi and plug it into another USB port, then re-run flash.
The long version:
This is NOT a lack of serial connection (I get initialization and the first Read). A serial connection exists, but the longer that avrdude runs, the more timeouts develop.
I thought this might be due to running the graphic interface, or possible voltage issues from having a keyboard and mouse plugged into the USB; I also considered problems with a long USB cable or a corrupt bootloader.
I bought a new Arduino Duo and short (2ft) USB cables. Swapping out the board and cable gave the same results as before.
I tried going into the Raspberry via SSH (without the graphic interface running) and still no change.
I then tried adding another power connection to the Arduino, with no change.
It was on a wild whim that I moved the cable to another port, and it ran clean on the next flash.
I then decided to see how much I could abuse the Raspberry and still get a good flash. Every time I started getting timeout problems, I moved the cable (with no reboot) and it went back to working (at least once).
I now have it back to the original configuration:
- Using the graphical interface (no SSH) and command prompts
- 6 ft USB cable (so the sensors can be further away)
- Mouse, keyboard and thumb drive plugged into USB; in addition to the Arduino
Flash works fine, I just pull the cable and put it in a different port and the next flash works.
Note: If SSH is acting up, try cleaning your device list on the router and rebooting the router. I also like using Putty from a second Raspberry.