tenfoot
I am not convinced this applies only to waves either. It vseems to be a general VST issue.  I have had several projects where synth patches have been lost, particularly after archiving then restoring tracks. 
 
Its a tricky one though. I am yet to reproduce it consistantly. 

Come to think of it, I have experienced situations where I've programmed quite intricate patches in Reaktor, recorded the audio and then turned the synth off. Later on I decide I want to revisit the synth and tweak the patch, but when I turn it back on everything sounds totally different to how it was when I first recorded the audio.

It's not the GUI the sound is reset to default of the plugin. I will look at VST2-VST3, but it needs to be fixed.

Hi
 
I'm not sure if this will be useful but at least it's worth adding that I am having the same problem.  I spent hours getting things sounding right in my mix and then the next day when I opened the project all my Waves plugins had reset to default settings. Many hours of work gone. It is incredibly depressing and I felt completely defeated.
 
However, I fixed it.
 
I don't know if this will work for others but I guess it's worth posting just in case. I immediately closed Cakewalk without saving (VERY important: Do NOT save!). Then I started Cakewalk again only this time I gave it a couple of minutes to load everything (some was cached, I'm sure, so it loaded faster than the first time anyway). Then I opened the project. All settings were back.
 
Last week I was saving while the plugin was open and on the screen (ctrl-S... twice, just to be sure!!) and I thought that worked but then when it happened again last night I came up with that new plan. So now I think it has something to do with plugin DLLs not being fully loaded before loading your project.
 
I noticed in the grey box in the bottom right corner (right after opening Cakewalk) it mentioned a dll, maybe WavesLib3.103_10.0_Win64.dll (or something similar), so I decided to just wait and make sure all that stuff was fully loaded before opening the project and then it loaded all the settings perfectly. 
 
I have no idea if that will work for anyone else but I HIGHLY recommend: Immediately after opening the project and before doing anything else, check a few important plugins to make sure your settings are there . If not, close without saving and reload slowly.
 
And if you aren't already doing it, I HIGHLY recommend making a backup of the project folder after you close it for the day!
 
UPDATE (in case this is ever useful): 2 days later all settings gone again. This time it was because I bought Ozone 8 and got a free one called Youlean Loudness Meter. Neither works in Sound Forge 11 for me. When trying the Youlean one a second time (oddly it worked just ONCE!) it always crashes Sound Forge (disappears off the screen completely) after hitting Preview. After that the Waves settings were gone in Cakewalk. 
 
I found that after I rebooted the computer and loaded Cakewalk and the project again (slowly!) the settings again came back.
 
Both of those plugins work fine in Cakewalk. (Ozone and it's Assistant are fantastic!)
 
Scott