Rather than messing with the cluster and glitchy chinese software for SKC retrieval, you can get SKC from your old ECU and then update it to the tuned ECU.
ME7 EEPROM tools command line program can be used to read/change/write the EEPROM .bin file which stores the ECUs SKC and immobilizer.
http://nefariousmotorsports.com/forum/index.php/topic,1168.0title,.htmlI also have a 2003 B6, I think the v1.31 eeprom tools worked better for me than the newer v1.40 though I dont remember exact issue.
you can sometimes read the EEPROM .bin over the OBD port but write changes must be done with the ECU in boot mode (out of the car, hooked up to bench harness). Either way, you will need boot mode to reprogram any changes back to the tuned ECU so need to get that setup.
See links to boot mode instructions from
http://www.nefariousmotorsports.com/wiki/index.php/Main_PageOnce you have a EEPROM .bin read of your old ECU, you can display the SKC and transfer it to the tuned ECU so immobilizer will be paired to cluster. Alternatively, you could just turn off the immobilizer on tuned ECU, car will run but downside it that you will then not be able to pair new key to the immobilizer in the dash cluster which has its own immobilizer. Both ECU and cluster immob must be active to pair a new key.
The command line ME7 EEPROM tools program can also be run via the GUI visualME7logger program, a bit easier to use if you are not skilled at command line program use. In this GUI with the EEPROM .bin loaded, the ECU SKC will display directly in plain text and edits to the SKC, VIN#, immobilizer can be made in the GUI interface. After any changes, be sure to update checksum on your EEPROM .bin before re-flashing it back to ECU in boot mode!
http://nefariousmotorsports.com/forum/index.php?topic=4830.0title=https://github.com/sbloom82/VisualME7Logger/