Ah sorry, I missed that part in your previous reply :)

I can see one of your problems is in the synth rack.. You only need one instance of TTS.
TTS-1 is a 16 channel synth. Having more than one inserted will cause confusion. 
You can quickly see which synths are being used buy checking the SOLO button in the synth rack. Delete all unneeded synths. 
 
And when you click on the INSTRUMENT ICON ( looks like a keyboard)  to the left in the track inspector to open the GUI the synth that opens is the synth that is assined to that instrument track. 
What I see is you clicked on track 13 and TTS-1 opens, correct? 
 
If I was you I would abandon using INSTRUMENT tracks and use a MIDI track. This is a classic case of why you shouldn't use instrument tracks. 
 
INSERT A MIDI TRACK above or below  each instrument track
Drag the midi from the instrument track to the midi track. Be careful not to shift in time. zoom in a bit. 
Now set the output of the midi track to the instrument VST you want to use. 

I don't know if this is related to your problem, but as a beta tester I did once report a bug in which deleting a synth from the synth rack that had MIDI-output enabled causes the routing of other MIDI tracks to get screwed up. Are you sure that you didn't remove a synth that had MIDI-output enabled? Here is the bug recipe:
 
Steps: 
1) Insert a MIDI track
2) Insert a synth into the rack with MIDI-output enabled
3) Set the input of the MIDI track to this synth
4) Insert another synth into the rack with MIDI-output enabled
5) Delete this new synth

Expected Results: 

After deleting the 2nd synth, the input of the MIDI track should remain set to the first synth. 


Actual Results: 

The input of the MIDI track changes to the previous synth in the MIDI input list (if one exists), or to Omni (if no other synth is in the list). 

I don't think I did, but assuming I did, how do I fix the remaining tracks so they are playing the correct instruments? And it looks like it's correct, that if I delete a midi track, everything else gets shifted... this hasn't been happening for the last several years I've been using Sonar, what changed and how do I fix that?

I might have to put it on my web page as I'm not sure how it will bode with putting 35 images in one thread. 

Ya, I've got dozens of screen shots on here and other forums that are now dead links because Photobucket is holding the ransom. So Imgur seems solid so far and not predicted to go down I guess. But the problem with that is the thread will disappear and be hard to find. I put the link in my signature so it will always be easy to find here. 
I've got tonnes of storage on my web site, Screen shots are not that large. It's way easier to work that way building these things as I have 100% control, plus I can update a photo with a better image or add text. 
 
I can also put some sample MIDI files to use. I tried CWP files but they open as a txt file with all the gibberish.
Any the link is in my signature-  Mr Tindog was one of the folks who I though might benefit from this. 
 
 

For PC
 
I kinda like Studio one 3....rock solid on the audio so far!...not doing any midi on pc...as it seems to always bring in issues.(mac works great with both)
 
Reason 9 has so much to offer, I have never had a crash using it for audio, but the vst thing is needing a bit more care with third party vsti, midi works just fine in that with their rack stuff in the software.
kind of deep learning what does what on the rack though..and how to route.
 
Magix has something but costs a pretty penny (waiting on Acid 8) ...reaper is a good go to , mixcraft might do?
 
Some say Steinberg...But I got nothing good to say of that company....well one...asio.
 
Cheers