Yes, an empty default tells SONAR use the "Default - All Plug-ins" layout. At least that is my best guess based on tests. The default layouts are built on the fly. There is a tmp written into my menu layout folder. Looking at the tmp, it appears to be the "Default - All Plug-ins" layout for the effects.

@steve cook: your #19 raises another thought. For a week or two, I have from time-to-time had a CLSID query pop up when I try to access various plug-in handling areas (sometimes even as the file opens). This always identifies three alternatives for Boost11, and I simply confirm that the third alternative is correct. I confess that I did not give this much thought, as the resolution was quick and easy, and Boost11 is in my default template so is loaded (albeit not always active) in most of my projects. When I have had these CLSID errors before they have typically been to do with an obsolete plugin where the replacement is already present in my system. Could this be anything to do with this new corruption of my MRU key and/or is there any easyish fix?
 

IDK if the CLSID issue is related or not. I am guessing about the cause of the layout issue.  A VST reset will rebuild the VST Inventory but can do nothing with the CLSIDs stored in projects. May want to review your scan path. Have you messed with the plug-ins in the excluded lists?

The VST reset has not changed the grey-out behaviour (nor has it fixed the CLSID issue, but you predicted that it wouldn't). The scan paths seem OK - the only one that seemed unfamiliar to me is a Cake Internal path, which seems mainly to contain PC modules, so I guess that's OK. I have never attempted to set a plug to Excluded or vice versa and the ones that are excluded are all Cake items that are themselves contained in the Internal path - I vaguely recall seeing a forum post some time ago that said this is normal and a byproduct of some change deliberately engineered by the Bakers (I wouldn't be surprised if it was one of your posts, Steve!).
 
I much appreciate your help on this, but I'm just going to adopt the workaround of never selecting "default" for the synth rack. It's all more Dark Star than 2001, it seems.

ChristopherM
It is not set by the other menus, because each seems to have its own MRU entry, which makes sens I suppose.

If I make changes to the main menu "Insert / Soft Synth" plugin layout, it is reflected in the "Synth Rack / Insert Synth" menu and the "Replace Synth" menu in the Browser Synth Tab menu (and vice versa).  So I wonder if you can  'repair' your Synth Rack menu by going through the main menu or the browser Synth tab menu.
 
Making a change in any of these three menus causes both "SynthRackSynths" and "PluginBrowserSynths" MRUs to be updated to the same layout file.
 
This is not true for the FX bin which uses the "TrackSynths" MRU.
 
I can't find what the "Synths" MRU is used for.
 

Interesting, but not what I am experiencing. The MRUs reflect the different layouts last used, so it is possible to have different layouts in use almost simultaneously. It only goes wrong for me if I select "default" in the Synth Rack.

ChristopherM
Interesting, but not what I am experiencing. The MRUs reflect the different layouts last used, so it is possible to have different layouts in use almost simultaneously. It only goes wrong for me if I select "default" in the Synth Rack.

Which update are you on, Christopher ?  I'm on Kingston, and what I described is definitely what is happening on my system.
 
EDIT :  I should add that during all the playing around I did to figure this out, it occured (only) once that the main menu "Insert / Soft Synth" refused to upate its layout no matter how many times I selected another layout through its "Plug-in Layouts" submenu.  Changing the layout from one of the other two menus fixed it and it hasn't misbehaved since.
 

Paul - I am on Manchester 1. I can't recall which update first brought this issue, which I suppose is because the fuse only blows when I select "default" layout. I don't typically do this, because I have specific layouts developed to suit my purposes.
 
I have checked again how my various MRU keys are updating and there is no question that they respectively show the latest used layout file instantly it is selected in the given part of Sonar. I can't seem to find a key for the ReWire tab, but that may be because nor can I find a way of creating a layout file for ReWire devices - this is anyway academic, because the only one I have installed presently is Melodyne. I don't have a key called Synths, so I can't comment on that, but I do have one called PluginBrowser, which has remained blank throughout. All of the others are pretty much self-explanatory and work as I'd expect.
 
[Interlude: The Cynic's Lament. Lugubre, ma non troppo] I vaguely recall when Sonar was something that I used for making music. These days, I seem to spend more time artificially applying stimuli to randomly uncovered inputs and then looking for randomly exposed outputs, then using WTF theory to discern what is going wrong. That, and installing updates, which rarely actually add any functionality that I ever use.

Christopher, I think I've finally figured out why we've not been experiencing the same thing. The trick is all about the "Instruments" button in the [PlugIns] tab of the Browser, the one which turns blue when selected. 
 
If this button is selected/blue, no matter if the [PlugIns] tab of the Browser is displayed and the button is then visible, or not, as when you've selected the [Synth] or [Media] tabs, what I've described occurs.  If the "Instruments" button is not selected, visibly or hidden behind the other Browser tabs, things work as they 'should' and are what you have described.
 
It remains though that three submenus always show the same plugin layout list.  These should not be the same as the plugin layout selected for the Browser's [PlugIns] tab, but if the "Instruments" button is selected, they will be.
 
I've posted a step-by-step description of the issue in the Problem Reports forum.
 
Sorry to have invaded your thread.  I ended up doing so trying to figure out what you were experiencing and encountering this other problem.  You should probably also submit a problem report detailing steps to reproduce your disabled Insert Synth menu item.
 

My insert synth never comes back, no matter what I choose for a menu layout or how I modify the registry.  But I do think they are related.  Here's the original thread on this (maybe some clues there)
http://forum.cakewalk.com/Insert-synth-greyed-out-m3244558.aspx
It's been happening since at least June, 2015.
 
A few things about mine, Insert Synth from the top/main menu does open a synth menu.  It's not quite right though, because its manage layout options don't appear to actually work.  When I pick any of the layout management options in the first item in the menu, the menu closes but nothing happens.  The only way to change the layout in use is to right click on an audio track and pick insert synth from there.  That version of the synth dialog, looks the same as what the main/top menu's Insert->Soft Synth looks like, but it actually works and I can change the layout.  Which then does change the layout that the top menu uses.
 
But nothing I pick causes the plus sign on the Synth panel in the browser to enable, Insert Synth is always gray.
 
This doesn't really effect my ability to use Sonar, since I can use the PlugIns panel in the browser to insert synths just fine.  And the top level menu, while its layout options don't work, does work to insert synths also.
 
My guess has always been it's some side effect of having many versions of Sonar on this same machine.  I've been using Cakewalk/Sonar for a long time (my current store history goes about to Sonar 6 but I've been using Cakewalk even longer).  This computer (built in 2010) has had every version of Sonar since 8.5 installed on it.  I currently have 2025 plugins according to the toast popup when I start Sonar (it's not really that high since I install 32 and 64 bit of everything plus VST2 and VST3, but it's still a large number).  No amount of re-scanning/resetting VSTs has seemed to help this issue though.  
 
This is a bug in Sonar, of that I'm sure, but there is no way to get through to anyone at Cakewalk that could actually look at why the Insert Synth in the Synth Rack is different than any of the other Insert Synths.