Erroneously light mode applied instead of dark, Gnome Shell 48.4, Also flatpak issues?

[Lemagex]

GNOME Shell 48.4 Kernel: 6.16.0-5 Arch Linux

Installed by cloning repo and running

./install.sh -r
./tweaks.sh -r
./install -i -r

reboot

./install.sh -c dark -l --shell -i 'arch' --darker -N mojave
./tweaks.sh -c dark -f darker
./tweaks.sh -c dark -F
./tweaks.sh -d

I am now getting only dark mode on libadwaita applications. I have tried running only

./install.sh -c dark -l

and

./install.sh -l

still stuck on light mode until removing WhiteSur.

Separately, at the same time this issue begun to occur, my flatpak applications are no longer whitesur themed, even after running the appropriate tweak switches and rebooting.

[Lemagex]

Findings: Switching from Wayland to X11 fixes the issue and my theme is restored... but only on X11, this wasn't the case previously. On X11, Libadwaita now shows correctly as whitesur dark, on wayland it shows as white. On X11, Flatpak now shows a theme at all, on wayland it shows no theme and falls back to default. On X11, Firefox is now themed again. It's treated on Wayland as though the window decoration colours (and the contents of ONLY libadwaita / wayland apps) are inverted it seems...

[Lemagex]

Confirmed this only happens with WhiteSur. I attempted to test another theme that supports libadwaita/gtk4 and it works without issue https://draculatheme.com/gtk

Maybe there was a change in gnome recently.

[vinceliuice]

Run ./install.sh -c light -l -f to use only light version

[Lemagex]

Run ./install.sh -c light -l -f to use only light version

I'm trying to use dark version but it only shows light version on wayland and dark on X11, I've even gone and purged the theme entirely and reinstalled it in dark, it still only shows light on gnome 48.4/wayland

[vinceliuice]

Then run: ./install.sh -c dark -l -f