You should have only 1 setup.exe followed by multiple .bin files which are the various chunks of the program installer for the base program its self. All other .exes are something else because your TS12 should install the add-ons via its internal download manager.
Regarding your registration.
Ensure that your username and password in MyTrainz is the same one you are using here, otherwise, TS12 will not show on your route line.
If you have problems registering, and or have used two usernames, contact the helpdesk via the link above.
John