Do you have (in preferences) the VST3 migration switches turned on?
If not, try that first (assuming you have Waves VST3 version installed).
If for some reason you do not have Waves VST3 installed, I suggest that you might want to get them installed.
I have Waves VST3 and X3b and the VST3 switches on and have not had a problem with older projects opening with retained settings.