Hi Noel,
Thanks for replying, sorry I seem to have let this post slip through the net.
I was able to narrow it down an instance of Guitar Rig on the master bus. I always have NI's Solid Bus Comp in there. For some reason, it will sometimes initialize with all of the controls set to zero. Makeup, threshold, dry level, wet level...all zeroed out.
I have also seen this problem on my reverb bus when I have a Guitar Rig based reverb on there. The project will load with the reverb's wet knob turned all the way down, and the pan knob turned all the way to the left, despite the settings with which I saved the project.
I think this may be a Sonar/Guitar Rig compatibility problem because I used the same effects extensively in Pro Tools and never encountered the same issue.