I ran into this today, and couldn’t find a quick answer online.
I was updating yasnippet to the current release, and there was an error on startup about dropdown-list.el not be able to be found. That resulted in Emacs aborting the startup process before it reached the settings in my .emacs file that define the color settings.
So Emacs initialized with the default colors (dark on light), whereas my custom settings are light on dark. When I then exited Emacs, it saved the .emacs.desktop file, which I’d thought was just the list of files. However, it also contains the color settings, so after I’d worked around the yasnippet issue, and started Emacs again, it used the default color settings (from the loaded ~/.emacs.desktop file) instead of mine in .emacs.
The fix was to remove the line that begins with “(setq desktop-saved-frameset”, exit Emacs and start it again, in which case the color settings will be loaded from ~/.emacs instead. The next time Emacs is exited (or just desktop-save is run), then the color line in ~/.emacs.desktop will be updated.
This is probably quite an edge case, but I thought perhaps others might run into this issue. I hope this helps.