Thanks for the replies.
I too have no idea what is happening. When the 328P is breadboarded, with DTR connected to the reset via a 0.1uF capacitor in series and a 10K pull up resistor I can select the Uno as the board in the IDE and it uploads many of the example sketches. With the 1284P chip breadboarded in the same way it fails with the errors shown.
I made the following observation:
When a successful upload on the 328P is achieved, the TX and RX leds on the FTI board initially flash a few times, pause and then flash for a longer period. It's as if the software is initially checking for the chip, the chip identifies itself and agrees to accept the code, which is then transmitted. When breadboarding the 1284P I get the initial flashes on the TX / RX leds on the FTI, but then the IDE pauses before the time out results in the errors.
I'm no expert, but it seems to me as if the bootloader is communicating correctly. I've tried different baud rates, but with the normal standard port settings.. I assume the optiboot loader uses the standard serial protocols ?