Why is it that my FIO cannot be programmed while connected to a breadboard? I have no other wires attached other than the FDTI serial port adapter. This seems to be something systemically wrong with the Atega328 when running at 3.3V. I can remove the Arduino from the breadboard and plug in directly without going through headers on the breadboard and it works fine. I have probed the TX/RX signals, and within the first couple second of plugging in the USB, the TX line from the Arduino gets stuck low. While monitoring the RX/TX signals, the only difference I see is the Arduino's TX line drops from 3.3V to 1.9V and goes back to 3.3V within 10 ns. When connected to the breadboard and header plugged into the breadboard, this tiny little glitch does not appear, and the TX line stays low and the software gives the stk500 error. My best guess is this is some sort of protection against sinking to much current through the TX pin inside the Arduino. I have tried a Sparkfun FTDI adapter and an OSEPP. They both have the same behavior, which isn't surprising considering this is an issue with the TX line in the FIO. I bought 2 more FIOs and they have the same problem. I tried a different breadboard, and different headers, same problem. I see lots of people online complaining about not being able to program Arduinos, and the user guide says the Arduino can't be touching anything metallic. I don't have this issue on my Arduino Pro, and I am changing the reference between 3.3V and 5V on the FDTI.
We need to know how you have connected everything in the breadboard to the Arduino.
Have you connected the Gnd of the breadboard to Arduino Gnd?