Just to throw this out there, when you enter your license in the License dialog box, it gets stored in a file on disk, inside of the configuration location for Sublime. If that file can’t be saved or gets disappeared on your behalf, Sublime won’t know that it’s registered.
If you use Preferences > Browse Packages
to open the Packages
folder, and then go up a directory, you should see a folder named Local
; inside of there is where the License.sublime_license
file is saved.
So, may be worth a quick check to see if there is any correlation between you asking and that file not being present (and if Sublime is actually writing it there or able to write it there when you enter the license).