Well I have just tried the same Vagcom setup to read Corin's Audi codes and with that you could get into the engine module and actually read and clear the fault codes. The Audi is slightly newer, but it does use the same 2 connectors so I suspect that the LED test that I'm doing is simply that, an LED test and not the fault codes. So, it doesn't look like vagcom is able to access my ECU even though it successfully connects. I will give it another go today.
Corin, I have cleared those codes now. Many of them may have been latched on if you switched the ignition on whilst things were disconnected etc. Best thing to do now is take the vehicle for a drive, over to me for example, and we'll connect it back up and see if any of the codes come back. Any that do will be hard faults that still exist.