Odds are the ecu that has the 200hp fe on it was crossed flashed with a different software version. Bosch uses a different software number for almost every different year of the same model. So for instance a 2003 awm b6 a4 has a 518af number, 2004 b6 a4 is 518ak and so on. There's even different software versions of the same code. 518ak can have v001, v002, etc. they are all very similar but slight changes in map addresses and slight tweaks between.
The behavior you are experiencing with the fan running with your tuned ecu in is a result of having the wrong year ecu in a newer car. I didn't check the part number but I believe this is from the 2002 year b6. It's has slightly different hardware in the ecu. Though if it was immo offed properly the car would start. You'd get a cel for missing speed sensor and some other stuff and the fans would be running as you described. Best bet is to make your own tune, toss the ecu you have to the side and check out the s4 wiki. There's a thread dedicated to stage 1 and stage 2 for your car. Read up and check it out.
Oh yeh, mine is a 51 plate and the mapped ecu was from a 2002, i see what you're saying, just that some of this map talk can go over my head a bit as i'm a mechanic not a programmer
