I have a .cpr file with custom colors that I want to save as default using the Project Colors Setup menu (shift alt S) but the store color set as default button is not working. I then tried to make my own custom colors and it still will not save. It’s beginning to seem like it’s a bug?
I’m on 10 Pro using Windows.
When I setup custom colors with info i got from:
“CUBASE TIPS - How to COLOR SHADE your TRACKS | MIXDOWN Q&A - YouTube”
As I followed those instructions, on the cubase Project Colors Setup tab and clicked on the Store Color Set as Default button - I also believed the button did not work, as you are saying. I found out that it is actually working! You see the thing is that the button does not “appear” to work because the buttons screen graphics do not change when it is clicked, to give the user feedback to let the user know that it worked - However Cubase has in fact stored the color set - same deal with the reset button. It is a bug, because it should “appear” to click to provide the user feed back, but the easy work around is to simply understand that it actually does save the color set. Give it a try for yourself.
I did try and on any new project or reloaded old project Cubase only has the stock colors… however the CPR file came from a 10.5 user and I’m on 10. I dont see why that should matter if it successful changed my colors… yet… it still didn’t work. 
All I can offer is that I was able to follow the steps in the “CUBASE TIPS - How to COLOR SHADE your TRACKS | MIXDOWN Q&A - YouTube” video to save the custom color set in cubase. And then I was able to opened my old project, then at the file menu under project color setup, presets options tab, clicked “reset color set to default” and then the custom palette is in my old project. I don’t think the version will matter. You could try this process of loading the custom color set in a NEW project, and just keep working at it. File ownership and different user permissions “possibly” could cause issues. Good luck.
Thanks for that additional feedback, and I too have this working now (in Cubase Pro 10.5). I was getting frustrated but realised I was making the mistake of then opening a template, which of course has its own colour palette and overrides the updated colour palette. Creating a new blank project shows the updated colours. 
Bindi
You can change to the new colors in the Template too. Since colors are retained at the Project level when you first open the template it will have the colors it was created with. But in Setup Project Colors/Options the button ‘Reset Color Set to Default’ will load your new updated colors. Then if you save the Template it will keep them.
And this: