Thought you might be interested to know that something similar happened to me last night.  I was playing around with TTS-1 and used the "MIDI Kill" button in Sonar because one of the notes was hanging.  After using the "MIDI Kill" button, TTS-1 couldn't see my MIDI keyboard input anymore and wasn't making any sounds. 
 
The fix for me was to add another synth to the project on a separate track.  This seemed to cause Sonar to "snap out of it" and then the input and sound to TTS-1 worked again. 
 
Not sure if this is related to your issue or not but it seemed similar.

Just by coincidence I also had a similar issue with TTS over the last few days.   I've been slowly replacing the TTS parts with other synths, so only drums and organ remain.   However, I could not get these remaining MIDI tracks to respond to real-time playing, even though I could enter notes into those strack and they would play back.
 
The answer for me was that some of the previous "dummy" tracks were muted to make way for the new synths, and as soon as I un-muted the original piano MIDI track on channel 1, the remaining drum and organ MIDI tracks worked as expected again.   I haven't dug in any further to see why, I just muted all of the clips on the piano track instead.  :)
 

Posting an update on this:
 
I've used X3 for two more weeks since the last post on this thread.  Every single VST (and DXi) I've wanted to use in projects has worked fine, both FX and instruments.  The Only thing that continues to not work is TTS-1.  It's really inconvenient to suddenly not have it available, since it's been my sketch pad sound source for a very long time, and sometimes instruments from the TTS-1 have ended up in final versions of projects.
 
The behavior persists of constantly losing sound, sometimes with notes delayed, usually with them never sounding out.  MIDI output is not selected for the plugin.
 
Re-installing from the X3 installer, and then running the Plugin Manager, made no difference.
 
If anyone has a new theory of what's going on, I'd love to hear it.
 
Randy B.

I know you've been inserting TTS-1 from scratch, but are you always starting with a custom project template, and have you built a new one starting with the default Normal.cwt that ships with X3? Also, have you checked your MIDI Prepare Using buffer? The X series defaults to 250 vs. the pre-X default of 500, and this causes trouble on a lot of systems, including mine.

brundlefly...are you always starting with a custom project template, and have you built a new one starting with the default Normal.cwt that ships with X3? Also, have you checked your MIDI Prepare Using buffer? The X series defaults to 250 vs. the pre-X default of 500, and this causes trouble on a lot of systems, including mine...

Excellent and super instant reply, as per usual Brundle - Thank you.  I meant to say that back when you posted this about the prepare buffer, I changed my setting to 500.  That was helpful, but didn't fix this particular problem.
 
I'll run a test with the shipped X3 Normal template, or Normal project file.  I haven't done that yet! - Everything I'm working on currently was started with 8.5.  This sounds like it's probably the solution.  Thanks - I'll let you know what the results are, so I can hopefully re-title this thread with SOLVED! in the subject line.
 
Randy

Everything I'm working on currently was started with 8.5.  This sounds like it's probably the solution.
 
I'd be interested as I have had  TTs-1 behavior like you are describing and all my projects are also from 8.5. 
the only solution was to delete it from the rack and re-insert it.