I bought it separately when it first came out and had to register the serial number on the MyTrainz Serial Number page but I don't think I had to register it when it came bundled with UTC or as part of TRS2006.Only one serial showing in my account.
Trainz Paint Shed V1.3 (Download Only)
AUPS-XXXX-CCCC-BBBB-MMMM-LLLL
Yes, it is a fake serial I'm showing.