@J-D The solution is that the Arduino Dock had a dead short (ohm meter, 0 ohms) to ground on the TX0 line.
I cut the pin and soldered a wire right to the board, and now it works.
I looked at the schematic, and no, the mini-usb does nothing but provide power.
Also, the 3 pins on the side connect to a mux that switches between the console on TX0 and the ATMEGA serial port, the Omega has to give permission by raising IO19 to program the ATMEGA.
Hard to believe another 3 pins could not have been added, to making it easier to program the Arduino. Also, for the price a serial to USB adaptor should be there, instead of the analog mux. 7.00 china Arduino knockoffs use a low cost serial to USB chip that works just fine (CH340).

Build 0.1.9 b149
Arduino mother board (don't get the silicon labs device, not sure if I should).
FTDI converter connected to serial port pins (it works on TX1 from the big connector)
Issues:
Serial port pins on the side (TX0) get nothing. In fact the TX pin is sitting a 0V (should be high).
The fact that is is at 0V says that either the HW is dead, or it never got set up.
Echoing to /dev/ttyS1 sends data out at 9600 baud on TX1, but S0 is dead.
(See reply below for solution)