Sander, I'm thinking this may be something specific to your system. There are many people using Waves without issues like what you're seeing from what I've read on the forum. I'd definitely try and contact Sonar support to see if they can help you on this.
Other than that, the only thing I can recommend would be to go into your preferences, VST and do a reset on the plugs. Then tick "rescan existing plugs", rescan and then see how it works. 90% of the time this fixes plug issues, but may not work for you. (remember to take the tick out of scan existing plugs after your done)
I just had a dealing with support today and let me tell you, I like to think I know what goes on with Sonar under the hood. As much as I know, I'm still clueless and found that my issue I reported was my own fault. Something that I completely missed was totally jacking my Waves plugs that would have been really hard to track down. But I was determined and found out it was totally on me. So you never know...I'm not at all dismissing that you have a problem, I'm just saying that quite a few times we can miss the obvious even when we are pretty sure we know we've done everything right. Then there's the other side....things that worked in X2 may appear to be broken in X3. This was part of my problem too.
"How did it work in 8.5, X1 and X2 yet it doesn't work in X3....it's X3's fault!!" Come to find out things are working BETTER in X3 so it caught the mistake that shouldn't have worked in previous versions. So it appeared broken in X3 when in reality, it was pilot error.
Just curious....do you happen to have any console emulation on any of your tracks or buses? If so, try removing them and see if it still happens. I wish I could be more helpful, but I'd definitely turn this one over to support by phone if you live in the USA.
-Danny