This is a rant.
Why in the name of all that is Good and Holy does Sketchup not save my shortcut preferences after I close the program???
I have had to reset my entire shortcut preferences 4 times today and I’m about to lose my mind.
/Rant
After you have modified your preferences you have to save your model before quitting SketchUp. If that doesn’t work your SketchUp installation is faulty or incomplete. Then you have to locate the installer, right-click, select “Run as administrator” from the menu, and when the installer has started, select the “Repair” button.
What does the model file have to do with settings that are saved into the preferences JSON files?
yeah, not needed. just close properly, no crash, just quit. preferences are independent from your actual file.
I also see sometimes that “you have to save as a template”. also no.
that is the solution yes. it’ll give proper access to sketchup so it can write your preferences files where needed.
I agree with @Anssi , if I move toolbars around or change/add a shortcut they don’t ‘stick’ unless I save. I’ve been doing this for as long as I remember. If I exit without saving a file everything reverts.
When I’m performing the ‘the dance of the toolbars’ once a year I usually save an xx.skp to the desktop and overwrite it as I go.
Yesssssss, I perform the RCAIAA ritual before you ask 
well, I do it without saving anything on a weekly basis on brand new installs. my trainees install sketchup, open it, we change the toolbars, move around a bit, then we quit without saving and restart with a fresh file (quitting allows me to show them that it’s all they need to change interface)
here. open sketchup, change a toolbar, quit sketchup WITHOUT saving.
reopen sketchup, the toolbar status was automatically saved upon quitting. because it’s in the preference file, not in the actual skp file.
edit : same goes for the mac version btw. with the difference that if you place toolbars or panels in forbidden areas (slightly outside of the screen, or on each sides of the dock), they’ll be moved / kicked to another screen.
So the “run as admin” is the only thing i haven’t tried, but surprises me a touch to be honest.
I save my models quite regularly as I am working on them throughout the day.
Some of my changes are saved some do not. so its not like none of the changes save, its just that they will be working, and then “all of a sudden,” (walk away for an hour, open another model and then come back to the model, close the model and re-open it) some of them stop working.