Thanks Alex,
I'm running the latest Waves, R9v14. Yes, they just released v15 today with AAX support, but I haven't seen what else may have been fixed yet.
I have rescanned VSTs after the X3d update. In fact, I have it set to "manual scan" and I rescan after installing/updating any plugins. (Which I've done several times during the 'Holiday Sales season') I did not do a rescan between saving the project and opening it again the next morning.
I've been using Sonar for about 5 years and never had this happen before. In this project, I have 3 instances of the same CLA plug (on separate tracks) and another instance of a different CLA plug (on a different track). The other three instances all had their settings intact. Only one instance lost my settings and reverted back to defaults. But, after reloading the project ALL of my settings were restored.
So, the settings were saved there in the project, but they did not load properly when I first opened the project.