I open the Platinum 'normal' template and make adjustments. I save the template and reopen it to check: changes are all saved as expected. However, when I open Platinum via my desktop shortcut to the exe file (my usual method for a new project), the default file which appears will show my changes with the following 2 exceptions, which I can repeat ad nauseum:
(1) My personalised instrument plugin layout will not be remembered - it reverts to Cakewalk default
(2) My console view layout will not be remembered (although this one is weird because it only happens when the console view is not the dominant view) ie I adjust some other parameter (such as the track view) before saving.
Can anyone else reproduce this?

> However, when I open Platinum via my desktop shortcut to the exe file (my usual method for a new project).
 
What is your desktop shortcut? Please paste the path...
 
How are you opening the project after that ? (Unless it's in the path).
 
What happens if you double click on the template file itself into Sonar or double click on it or do File/Open?

The desktop shortcut I use is the one that cake offers by default -  a link to the .exe file ... 
"C:\Program Files\Cakewalk\SONAR Platinum\SONARPLT.exe"
 
I double click the icon - Platinum opens with a new file ready to go (the normal template), ready to be saved as a Platinum file. Whether I use that or if I use the quick start menu and choose new project, or go via 'file - new', I always get the same result - which is my plugin layout not being retained.
 
I've also tried opening the template direct (as a template file), then saving as .cwp file - but it still does the same.

Are you sure you are saving / opening the right template?
Did you create this template from an older version of Sonar which case you should start from scratch using no template.

Definitely the right template - created from scratch. Other changes I make to the template are remembered and show in the new file.

As I'm not in front of Sonar and this isn't getting much attention other than what I'm posting, I'll pop it into the Sonar forums to get more eyeballs. It could still be a bug so we can move it back to problem reports if necessary.

The first part sounds similar to something I have been experiencing for a very long time over the past few years. I made a custom "Instruments" setup for VST, but when I open Sonar, the normal template loads with the default cakewalk list. I have to reselect it every time.
 
This is what works for me. It involves an extra step, but it's way less tedious than clicking on the custom list. Instead of defaulting to plugins -> instruments, try making the normal template plugins -> audio fx using the buttons above the list, and below the "Media, plugins, Synth" line. This is how I have it set up, and all I do when I open the program, is switch to Instruments, and it remembers the custom list of virtual instruments.
 
I hope this information is helpful.

Regarding (2), just check to see if it's a locked screenset . Changes will not persist if this applies

Alphadeus, I tried your suggestion and it does keep the personalised instrument list intact (which is good), but then still loses the console view layout.
 
Jonesey, I checked for a locked screenset but none present, so I'm still looking for other possibilities.

Alex, even though I was extremely confident I had constructed the template from scratch, after your suggestion I went back and did it twice again just to make sure, once beginning with a new blank project and turning it into a template, and secondly with an existing Cakewalk template (16 track) and customising that. I still had the same result with both.