I have the same issue, Tracon2012se is my first crack at the tracon stuff ; i do have tower 3d pro, so i was able to copy and paste the (for instance klax) shedule.txt and rename it within the tracon folder , and it works fine for KLAX, but nothing for the sattelite airports, so i dont think that is a very good "fix"
I downloaded the bundle pkg on steam that has ATL sector, dubai, frankfurt, london 1&2, new york, and norcal dlc.
When i tried the RT on the new york sector, the first flight comes up, however, it proceeds not to move on the screen, and no other aircraft show up...
I mean , if this is an issue with folks who bought off steam, perhaps it would be best if I could just download directly, install everything, all my dlc after and then the RT...it seems something is missing or not functioning correctly when you download the RT for the 2012SE.