I actually have zero controllers checked on my system for X3, and had no issues playing sounds after stopping playback of the project.
The test project I refer to is a new project, using Normal template. I inserted a single instance of TTS-1, then inserted 3 different stereo audio tracks and 3 different regular midi tracks.
I kept piano on TTS-1 channel 1 (first instrument at the far left), changed the 2nd instrument to Organ, and the 3rd instrument to Fretless Bass.
I then set the audio track routing assignments accordingly, and all midi tracks were already set to output midi to TTS-1, but I did set Midi Output Channel values for the 3 midi tracks to be channel 1 for piano, channel 2 for organ, and channel 3 for bass.
Soooooo, with the above, I captured some goofy midi notes for each midi track (all 3 instruments, all playing something different, but at the same time).
After completing the recordings, I hit playback, let it play for a few seconds, then hit Stop on the transport bar, which did stop playback, as expected.
I was then able to click on any one of the midi tracks (which uses the Sonar default of setting midi input echo 'on' when that midi track comes into focus). Each midi track played the appropriate instrument when I clicked on that instrument's midi track, as expected.
Sooooo, I do not experience the same problem as you have posted, using X3 and TTS-1.
Is it possible you do not have midi input echo 'ON' for one of these midi tracks you are not hearing sound for? You have to make sure you firstly click on a midi track that has its output assigned to TTS-1, and you secondly have to make sure that when you DO click on that midi track that the Midi Input Echo On button is lighted for that midi track. (if the midi input echo button for that track is not lighted - when you click on the midi track - by clicking on the track number at the far left of the track, then you most likely do NOT have the Sonar default set to Always Echo Current Midi Track set properly - this is set in Preferences>MIDI>Playback and Recording).
I hope the above helps.
Bob Bone