Interesting to hear other people report this now, I did feel like I was somehow doing something wrong or was cursed, judging by how few people mentioned in on the forums before. Maybe we should have kicked up a bigger stink about it, lol!
As a beta tester it was a constant source of frustration that I couldn't come up with a recipe to recreate the problem. And it seemed so random - sometimes these synths and plugins would load fine, other times they would load flatlined. Someone else on the beta team with the Quadcurve problem said they think they saw it happen after moving the playhead in a project, so that might have been a clue.
As for the Waves issue, I did find a promising clue not long before Cakewalk went kaput. I was able to capture on video a band of the Q10 moving without touching it, along with a recipe of how to recreate it. Check this out:
I discovered it quite by accident. I'd opened the Q10 to make an adjustment, and after wondering why I couldn't hear any change in the audio, I saw that the ProChannel that the Q10 was hosted in was turned off. When I turned it back on, the band I'd adjusted moved on its own. I think the same thing happens with FX bins as well. So there you have it - an illustration of how turning on a ProChannel (after having made an adjustment to the plugin with the PC turned off) can send a signal to a plugin and change its settings.
So that got me to thinking about how these plugins were being changed. I don't think it's that Sonar is not saving the settings in the project file - I think it's more likely to be that something is happening as the project loads. Could it be that as Sonar initializes your ProChannels or FX bins, these stray messages (whatever they are) kill or vandalize plugin settings? And maybe something along those lines is happening when synths are initialized in the synth rack as well? Or maybe that's not the case at all, and the problem in the video is totally separate!
I submitted the above as a bug, and the Bakers were able to reproduce it. And then Cakewalk was no more. Daaaaamn......