Hey, so I had the same issue crop up a couple of times now on my PT 8 HD Mac computer.
The first time I noticed it was when I opened some mixes up that I had done on a different computer (same PT version and Mac OS). All of the SSL and CLA plugins had defaulted, tho the other Waves plugins I had used were how I had left them. Since I hadn't gotten too far on the mixes and was gonna tweak them anyways, I assumed (I know what that does...) that it was because I had saved them as a preset on the other computer and they didn't transfer over.
Last night we had a tracking session. After the first song, we took an hour to dial in the sounds with everything, so that I could just save a template and we could start flying from there. However, everytime that we opened a new session, SOME of the Waves plugins would default back to its orginial setting (4 out of 7 Ren 6, 3 out of 4 CLA-3A's, 1 out of 2 CLA-2A), along with all presets disappearing in the menu, both User made and Factory.
I am going to try and reinstalling Waves, but I am REALLY hoping that I don't have to reinstall PT... Any information PLEASE!!!