Went into Subaru service today. They hooked up the ECU to the factory diagnostic system and it appears my ECU is completely stock and not modified in any way.
We also tried dash command on 2 other legacy's while i was there, one newer, one older.
The older Legacy worked 100% while the newer Legacy wouldn't even establish a connection.
It appears at this stage that dash command doesnt support Subaru's (or at least Legacy's) past about 2003. I have however contacted the PPE techs again and I'm still hopeful of coming up with a solution and getting it working. It's a fantastic little program!
If your Audi has definately been re-flashed then I suppose it's possible that it could be causing you issues.
Anyways, good luck for getting it working. Hopefully it won't take too much