From the PDF manual on page 1581-2. There is an option to link clips. Not sure if this links parameters as well but try the different options to see what happens.
 
Clone Track(s) dialog
The Track view Tracks > Clone Track(s) command opens the Clone dialog box. Use this command
to copy a track or tracks to a new track or tracks. The Clone dialog box has the following fields:
Selected Tracks
This field lists the tracks that are currently selected.
Clone Tracks
• Clone Events. Check this check box if you want to copy the MIDI and audio clips in the selectedtrack(s).
• Link to Original Clip(s). Check this check box if you want the clips in the new track(s) to
become linked clips with the identical clips in the original track(s).
• Clone Properties. Check this check box if you want to copy the properties of the highlighted
track(s), such as the name, output, channel, etc.
• Clone Effects. Check this check box if you want the new track(s) to use the same real-time
effects that are patched into the original track.
• Clone Sends. Check this check box if you want the new track(s) to use the same sends that are patched into the original track(s).
• Repetitions. The number of tracks you want to create from the selected track(s).
• Starting Track. The track at which
 
 

It's not a bug, it is intended behaviour, which is why it's in the manual.

My quote is from page 320 - copying tracks.

While there doesn't seem to be a Control Group option in the Clone dialog what is being described is actually Selection Group behavior I won't paste the entire manual entry (it's long) but it is on page 914 of the PDF manual. Check to see if somehow the track parameters got added to a Control Group.

Beep, have you read my posts? When you clone a S.I.T. it only inserts a new MIDI track, linked to the same soft synth, so the effects are not exactly linked, they are the same effects.

jb101
My quote is from page 120 - cloning tracks.

Just read it. That is ridiculous. I guess they could simply call any bug "intended behavior" by putting it in the manual 
 
Let's take a look at their statement "When cloning an Instrument track, a new MIDI track is created and assigned to the same soft synth as the cloned instrument track." I just tried this, both in the project I'm working on and in a new blank project. In the project I'm working on, cloning an instrument track just creates another instrument track. In the blank project, cloning an instrument track creates another instrument track, plus an extra track that has the track icon Sonar gives to the audio part of the track when you split an instrument track. So I don't know what's going on there - cloning the instrument track gives different results in the new project than the project I'm working on. Also, in this new project, if I split one of the instrument tracks and then select "create instrument tracks" to rejoin them, I get the "Making an instrument track requires that a single audio and MIDI track are assigned to the same synth." So if you split them, you can't rejoin them. 
 
Anyway, if it's just the case that cloning an instrument track "creates a new MIDI track" then why wrap that new MIDI track up in a "new" instrument track that really has its audio part linked to the parent track? What is the point of having a second set of mix controls that are linked? If the user only wanted to clone the MIDI part of the track, then surely they could simply split the instrument track, clone the MIDI part and then rejoin the original instrument track. The whole point of an instrument track is that you get a single unit which handles both audio and MIDI. So the expected behavior when you clone one of them is that you get a brand new instrument track that is identical to, but which performs independently from the parent track.
 
So I guess Cakewalk's logic is that if someone wants to clone an instrument track, all they really want to do is to create a new MIDI track with the same clips in it, and have it output to the same synth instance. I'm guessing that this is not what they want at all, and if that's what they wanted then they wouldn't even bother with instrument tracks in the first place.  

Never saw the behavior before but I do not use simple instrument tracks. This looks like another good reason to avoid them. You could try splitting the track before cloning.
 
When something unexpected happens and I want a complete do over without losing the current work, I save the current project in the project folder under another name. Usually the base of the name is the same as the current project with something added to note what happened. It might also be the case that I retrieve one of the copies of the project made by the versioning system to use as the current project.

Ah... yeah I don't use simple instrument tracks either so IDK. I figured wee were just talking about clones in general. Seems odd SITs would behave differently. Sorry if I added confusion.

SITs have always been different. Some people like them and use them. I did not see much value to them when they came out. Even though they have been improved upon in every version of SONAR since their release, they still exhibit strange behavior just like the subject of this thread. If they worked just like an audio+MIDI track that would be one thing but they don't. Why chance it?

I only tend to use S.I.T. when I am sketching an idea out, and replace them with synth and MIDI tracks when I get going. I guess that's why I've not noticed this.

Mostly I clone audio tracks, e.g. to process a bass part as separately as D.I. and through an amp sim.