FF 97.0 Themes revert to white whenever relaunching FF
I love that you added a proper dark theme, and also even more-so one that is supposed to follow the Windows theme (System Theme - auto).
However, whichever I select it defaults back to basic White theme when I reopen Firefox.
I used to have a custom Firefox Color theme, which disappeared after the update to 97 - but the new Auto and Dark are perfect. Although not cool to blow away a theme created using FF Color - lucky I was OK not using it.
Looked at various forums and sites and as of yet not found any reports.
No custom .js files being used, just the prefs.js
Yeah, I certainly empathise with this as well.
The reason is due to a new auto theme detection implemented from Firefox 96.0 which checks the style of one's toolbars for a custom theme. Then it applies styling accordingly to what shade is detected. For me it was the other way around, with a dark theme when I wanted the UI to remain light themed (other than on the toolbar itself). It all depends on the brightness of theme we each use.
Looking into this, I managed to find a solution using AutoConfig which allows forcing preferences to be applied even when opening a new browser window (or restarting Firefox completely).
See this post here for details: https://support.mozilla.org/en-US/questions/1360389?page=2#answer-1479952
Since you wish to keep a Dark mode, the method will be slightly different than explained. This will require setting a value of 0 instead of 1 inside the firefox.cfg file. The custom rule is then what locks down the preference to tell Firefox which theme is desired at all times.
Hopefully this might help you.
If you have uBlock Origin, one of its settings relates to the theme. Perhaps one of your add-ons has something similar.