Hello forum, before posting I searched and read until my head cannot take it anymore.  I am left with bits and pieces of puzzle to put together.  But that's good for learning.

I recently purchase a 2003 ALLROAD 6-Spd.  I got the car with 1 key.  I purchase a key fob with a blank key.  Got the key cut by a locksmith and then try to program it with VCDS.

I use ArgDubs tool to read the EEPROM data from the ECU and have success.  Got the SKC from the file and enter it into VCDS immo adaption.  I tried for about a day and it would't accept the login pin. 

Try next day and then it took it with no problem.  Since the original key was in the ignition I did that one first.  The immo light goes out.  This means that the immo is now matched to that key.  Remove key and insert the new key as instructed by VCDS and nothing happens.  The immo light just blink away.  I then close the controller in VCDS, thinking maybe something is wrong with the new key since I did not buy it from the dealer.  Try another attempt and immo will not accept login. Now both keys don't work and car wont start.  I also noticed when reading the immo, I get "Bitte Address" instead of readable information.  Also upon looking at the hex data from the dump, the ECU number ends with "551S" but on the casing it prints "551R"

For the record, the car drives like a stage 1 tuned car but I have no idea who the previous owner is/was.  Could it be that the ECU was chipped with a S4 non immo file and thus cannot store immo data?  On removing the ECU it still has the tamper proof tough stainless steel around it so If it was flashed, it had to be over OBD.

Any ideas would be grateful.

If what I mention could be the problem, can I re-flash the ECU with a genuine stock ME7.1.1 Allroad 6-Spd file and try key adaption again? (assuming I know the SKC to this new file)

When you scan immobilizer (25) if it says "bitte address 17" it is indicating to use address word 17 for instrument cluster instead of 25 for key programming and immobilizer adaptation.  Later cars you actually use 25.  If the car has kessy it may be through address word 05 but I haven't actually programmed any kessy keys.

If you still have a problem try programming only 1 key at a time.  If the old one will program but the new one will not you may have a key issue.  Take a look at the immobilizer value blocks 21-24 in instrument cluster to see if the key is programmable.