Thanks everyone.
So in short, is there a way that I can prevent this from happening at this stage? My take on all this is that it's being worked on but the problem remains? I'm almost thinking of leaving Waves plugins out of the picture all together for this project. I did a full reinstall of my operating system, DAW and plugins and in the process lost many of my presets anyway. I don't fully know where my mixes are anymore :(
As Mike V said: "So in the interim the way to manage your presets is to use the plugins own preset picker to open existing ones and save your own presets."
I had been doing this but it wasn't eliminating the need to go through and re-select all of my presets whenever I opened a project. 5-10 plugins per project say, it gets really annoying to say the least. I really did not expect this from a brand new DAW and latest version plugin bundles that are so widely used.