Comment 8 for bug 1993874

correct, and this issue occurs when the Appearance tab ob th Settings app is activated (or Settings open with Appearance being the previous section) so the issue is likely to sit within the init part of the code of the Appearance tab which seems to be resetting (or do an action which causing the reset) the theme.

Also, if you open Gnome Tweaks, you will see that when selecting Dark via the quick menu, the themes are changed to *-dark". if you do the same thing using Settings, the theme isn't changed at all.