Although the files for the layouts are still in their original folder, and have all the entries expected, the layouts don't show up either in the drop down list in the Plugin Manager, or in the plugin browser in SONAR. I had this some time ago and traced it back to having .NET 3.5 installed - have removed this but still the same problem now.
 
Anyone else seeing this?
 
Any ideas for a fix?

Is the "Plug-in Layouts" path correct in Preferences > File > Folder Locations?

Yes it is. The symptoms are two fold:
 
(1) in Plugin Manager, the menus don't appear in the drop down list but you can open them directly. Once you do anything to them/save them they stay in drop down, but if you then open another, only the currently open one shows in the drop down.
 
(2) in the main program, when you try to select the menu you want, the default Sort by Category, Manufacturer and Type all show, then there are TWO divider lines (i.e. the original two, but with nothing there). The custom menus simply don't show and therefore can't be used.
 
Having not actively worked on my music for the last week, I can easily try going back to a previous backup before I started the process of gathering all the Sonar downloads (landing up reinstalling quite a lot) and also prior to an update to some Waves plugins to see if that was the cause. But if there is a known fix/registry fix/etc. that I can try before, that would be much appreciated in saving me some time :-)

It's a long shot, but do you still sometimes use 8.5.3?  There is an incompatibility between newer versions of Splat and 8.5.3 in their saving/usage of layouts.  If any of this makes sense for your case, I can try to find some recent posts that have the details.

Yeah, that would be my next guess. Cakewalk broke backward compatibility in the Plug-in Manager some time ago. Not only with 8.5 but X3 and older!