I don’t think I’ve seen this in WL 9 + the latest update to ProQ. I did have problems in WL 8.5. I haven’t used the WL preset system for individual FF plugs, I save the preset from within FF. But saving/recalling a plug-in chain in the Montage FX window has been OK. I haven’t done much with the Master Section in WL9, as I don’t use it as regularly.
No problems here with Pro Q2. Had an irritation with Master Rig which seemed to be at default setting after restarting Wavelab but on clicking on the scene buttons the settings were still there, audible + visible. Is it maybe just a graphic glitch, GUIs not updated?