I wasn't saying that to be spiteful; I was asking a genuine question. What do you use that thing for, if not to copy tracks? Also, I'm not sure I understand the dire within the Note left at the bottom of the cloning page. What does it mean to have the same soft synth assigned to the cloned track that would merit never cloning a track?
 
Also when I cloned it, I went in and edited each synth. I just used the other track's synth as a starting point.

It may not be the problem but cloning instrument tracks is a big red flag. Cloning instrument tracks has been the subject of several lengthy threads. I use instrument tracks all the time. Their implementation has improved much over the years. That said, I avoid cloning them preferring to split the instrument track then clone the Audio and MIDI tracks as needed.

+1 Scook. Great advice.

I avoid cloning Soft synths at all costs. Instead I use Track Templates (may even lead to the same problem). But they are just as fast. To be perfectly honest, 75% of my Projects are Audio So when I need to insert a synth I use the "Insert Synth" menu.

It's important to set the track input to the whatever your midi device is. This is a per-track setting. I generally set to "None" which most of the time only plays the currently selected track. Every so often an unrelated track also plays and when I look "none" has been changed to e.g. my main midi device. Not sure why that happens and if I'm not understanding how properly configure Sonar.

ampfixer
I avoid creating simple instrument tracks because things can get confusing. If there are 3 midi tracks going to 3 instances of Z3ta it's easy to put each on it's own midi channel and prevent cross talk. If the 3 midi channels are going to a single instance of Z3ta then you will likely get interaction.

 Okay, how do I check to see whether or not this is happening?
 

ampfixer
Another thing that could cause interactions is if the tracks in question are being echo'd. Try turning off the echo function on each track and see what it does.

 
I'm using SONAR Home, so the only options I see for this are Input Echo = On or Input Echo = Auto Thru. Which should I do?
 

I found out something new about the problem.
I started up the project again, and it was working just fine: nothing weird. So, I continued work as normal. After some editing I found that it happened again, so I started getting frustrated.
 
At the time, my tracks were organized in the following manner:
 
Bass
Drum Kit
Echo (Z3TA+ 2)
Whine (Z3TA+ 2)
Air Long (Z3TA+2)
Air Short (Z3TA+2)
Piano
High Air (Z3TA+ 2)
 
High Air was added to replace Air Short, which was the first track to go.
 
In an effort to remove the Short/Long issue, I decided to remove the Air Short track and make a brand new synth. However, at this point, I was having problems with two different tracks trying to use the same preset (annoying). Eventually I got that ironed out, but I still don't know about this input/output stuff. I just kept explicitly selecting the track, then clicking on the Synth button in the UI, as opposed to just clicking straight on the synth button, which seems to cause all kinds of chaos and confusion.
 
After that, by a means I still haven't managed to discover, it happened again; Whine had taken over once more. I got sick of that, and started removing tracks I wasn't using, starting with that stupid thing. Then the strangest thing happened. When I tried to play Long again, Echo's sound would play instead. So, I removed Echo, then tried to play again. I was detecting a pattern at this point, so I started lower on the keyboard (Bass C) This time, a drum hit came out. It seems like Long is directly linked to whatever track is directly above it. However, I still don't see anything in the UI depicting such an attachment. Additionally, I have not cloned that many tracks, so it doesn't seem like it's a cloning issue anymore.
 
To be fair, I started messing around the Matrix view, but since I didn't really know what I was doing, I deleted the only row I made.
 
What the heck have I done to merit such behavior?