pharmachris:
The loopback test works fine, I get back in the window everything I type in the text field
If loopback is working, STOP doing stuff to the 16u2. The loopback proves that chip is working.
pharmachris:
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,
Flickering tell us the bootloader is running. However. Solid sounds suspicious, it should turn back off. Because of how of the LED is implemented on the R3, it is possible for it to get stuck on, but it rarely happens.
Do you have a volt meter? You might measure the voltage on Pin 13 when the LED is solid. That'll give us an idea if it is actually solid-on or if it is flickering faster than you can see.
Something else to double check, which board do you have selected in the Board List. You might try switching between Uno and Duemilanove.