Well, FWIW, this exact thing just bit me.
 
I was setting up a template project and added Kontact with a track folder and a MIDI track.  I did not add an audio track because I was going to add them once I had reconfigured the outputs in Kontakt.
 
At any rate, I ended up with the exact same behavior.  Adding an audio track that listened to Stereo 1/2 of Kontakt restored sanity to Kontakt's mixer.  I don't know if this is relevant to your issue, Sharke, but I thought I would throw it out there for you.
 

sharke

robert_e_bone
@sharke - howdy and good morning.
 
By any chance, did you save off your settings in Guitar Rig as presets?
 
Also. what information can you relay as to how you set the instance(s) of GR for this project (and the loaded sound for each instance)?
 
Bob Bone
 

I can save the settings as presets and load them every time I load the project, I guess that's a workaround. Really, the settings should be saved with the project and loaded flawlessly with it, regardless of whether or not it's saved as a preset. You should be able to fire up GR, load some effects into it, and Sonar should remember what's there and how they're set. Or you should be able to load a factory preset and tweak the settings. That's how it works on the whole, but Sonar occasionally zeros the settings out. It would be less confusing if it happened every time but it doesn't. Anyhoo, I'm not suffering from the problem right now for the simple reason that I've stopped using Guitar Rig in Sonar (until such time as I forget that it doesn't work properly again!). My main problem at the minute is with the Kontakt Drummer libraries. 

I had a similar issue with losing presets with Kontakt - which had never happened before.  This was about 8 months ago.  I had installed Sonar or Kontakt over again, for some reason that escapes me this long after (sorry), but I DO recall that when I had done that all the Kontakt multi-rack settings associated with my projects were gone.  Just gone.  As I am typing this, I am beginning to recall that it was Kontakt I re-installed, because I had been believing that Sonar would save the preset values with the project data, and I distinctly recall the surprise that I had to rebuild the multi-racks.
 
I believe (with no concrete evidence) that for my situation, that somehow the re-installed version of Kontakt looked different to Sonar somehow.  I don't believe the loss of the settings was something Kontakt did, because I had taken no action in Kontakt to save the multi-racks I had set up.
 
I also do not think it was Sonar's 'fault' for my predicament, because if I had saved the multi-racks off as presets, I would not have had the issue, and the most I would ahve had to do was to reload the multi-racks presumably once, for each project, with Sonar once again remembering the settings for next project open.
 
I do not know if any of the above applies to your GR situation, but it's all I have to offer.
 
Bob Bone

robert_e_bone

sharke

robert_e_bone
@sharke - howdy and good morning.
 
By any chance, did you save off your settings in Guitar Rig as presets?
 
Also. what information can you relay as to how you set the instance(s) of GR for this project (and the loaded sound for each instance)?
 
Bob Bone
 

I can save the settings as presets and load them every time I load the project, I guess that's a workaround. Really, the settings should be saved with the project and loaded flawlessly with it, regardless of whether or not it's saved as a preset. You should be able to fire up GR, load some effects into it, and Sonar should remember what's there and how they're set. Or you should be able to load a factory preset and tweak the settings. That's how it works on the whole, but Sonar occasionally zeros the settings out. It would be less confusing if it happened every time but it doesn't. Anyhoo, I'm not suffering from the problem right now for the simple reason that I've stopped using Guitar Rig in Sonar (until such time as I forget that it doesn't work properly again!). My main problem at the minute is with the Kontakt Drummer libraries. 

I had a similar issue with losing presets with Kontakt - which had never happened before.  This was about 8 months ago.  I had installed Sonar or Kontakt over again, for some reason that escapes me this long after (sorry), but I DO recall that when I had done that all the Kontakt multi-rack settings associated with my projects were gone.  Just gone.  As I am typing this, I am beginning to recall that it was Kontakt I re-installed, because I had been believing that Sonar would save the preset values with the project data, and I distinctly recall the surprise that I had to rebuild the multi-racks.
 
I believe (with no concrete evidence) that for my situation, that somehow the re-installed version of Kontakt looked different to Sonar somehow.  I don't believe the loss of the settings was something Kontakt did, because I had taken no action in Kontakt to save the multi-racks I had set up.
 
I also do not think it was Sonar's 'fault' for my predicament, because if I had saved the multi-racks off as presets, I would not have had the issue, and the most I would ahve had to do was to reload the multi-racks presumably once, for each project, with Sonar once again remembering the settings for next project open.
 
I do not know if any of the above applies to your GR situation, but it's all I have to offer.
 
Bob Bone

This makes me afraid to reinstall my Waves plugs from scratch, which I've been advised to do to fix the problems I've had with them in Sonar. Someone in another thread said that if you reinstall your Waves stuff then Sonar won't remember any of your Waves plug settings in your projects, so you would have to go through all of your projects and save all of your settings as presets first. For a project that has upwards of 30 Waves plugs that's a hell of a task - multiply that by multiple projects and it's a nightmare. It also makes me worry about buying and setting up a new machine, which I intend to do in the next few months. 
 
In your case, I'd like to see how the multi-rack info is saved in the project....I assume that it's a combination of the disk location of the libraries involved along with their configuration in the rack. I can't understand how installing Kontakt again would make it look "different" to Sonar - after all, surely all the relevant stuff is either in the .dll or in AppData\Local\Native Instruments\Kontakt. Unless you're specifying otherwise, exactly the same stuff is going to be installed in exactly the same place as when you first installed it. Wish I knew more about these things though.