I'm having the problem with a few of my plug-ins (both VST and AU versions). After working for awhile and getting plug-ins set up and what not, I'll save and finish for the day and close everything. Upon reopening the session, several of my plug-ins will be at the default settings. I havent' noticed this happening with any Presonus or Waves modules, but the plug-ins that are causing me the greatest grief are the PSP E27 and the AlyJames EPROM2. Not only will they be at the default settings, but any presets I may have saved in the plugin inself will not be there (I can only reload presets I've saved my own folder), so it seems the plug-in is reinitializing every time.
I've check and this does not happening in Logic or Adobe Audition with the same plug-ins.
I'm running the latest S1v3 pro with no pirated plugins
mid 2011 27in iMac 3.1Ghz i5 with 32GB ram and 2GB video card
OSX Yosemite 10.10.5
Motu 828mk3 with latest drivers and firmware