Yeah, that shouldn't have done anything since you can't program the bootloader without a programmer.
Thanks for clarifying that.
In answer to the question if the pin 13 led flashes on reset, yes it does, it flickers on/off a few times, the goes dark for a sec, then lights solid from then on
The firmware i am using on the 16u2 is either 'Arduino-usbserial-atmega16u2-Uno-Rev3.hex' or 'Arduino-usbserial-uno.hex' I have used them both without success, currently the r3 version is installed.
The loopback test works fine, I get back in the window everything I type in the text field
The only other thing I can add is that when I attempt to upload a sketch, the pin13 led flashes a few times and goes straight back to solid, and the Rx led flashes a few times, then nothing. I get no activity on the Tx led