For those who don't want to go through the hassle of Little Snitch installation/de-installation (though I kind of like having it, so I kept it), this is a response I received from the developer. It's a terminal command to update the boot-cache. I used this on my laptop yesterday (it didn't have the problem but I figured, "What the heck?") and it didn't appear to cause any problems. I'm still focusing on the permissions issue because macOS Sierra removed the ability to repair permissions, and I've fixed a lot of problems in the past by repairing permissions.
If someone is adventurous and wants to try this, it could be all that is needed to fix the Spaces/Fullscreen problem. Note: It takes a number of seconds (20?) and all sorts of text will fill your Terminal window; do not freak out!
I would restart after running it before trying to go to Fullscreen.
If anyone with the Spaces/Fullscreen problem tries this, please report it back here. If it works, I will report it back to Apple Support; it may help them fix the problem at the system level.
Here is the response. You can simply cut and paste the sudo touch command, but you will have to put in your Password at the next prompt to get it to run:
thank you for your request.
I would assume fixing the permissions for the /Library/ folders does not interfere with your issue, but since Little Snitch updates the boot-cache in order to install its own kernel-extension, it might be the effect that some corrupt system kernel extensions are updated coindicentally.
You can trigger a manual boot-cache update via the following Terminal command:
sudo touch /Library/Extensions/ && sudo kextcache -v 6 -update-volume /
this probably reveals some errors in case.
On the other side, if this is an issue of kernel extensions it is a bit odd that it only happens on certain user accounts. This would of course more lead to the assumption that some preferences at ~/Library/Preferences/ are to blame, but the Little Snitch installation does not alter any other plist files in there of course.
Hope this helps at least a little.
Best regards,