If you set Dark or use GTK (with a dark theme) it doesn’t keep this preference when you go back into brave. It will show GTK or Dark but it’s still Light theme anyway.
This has been happening since update to 1.52.117 on Linux Mint 21. Was working previously. Both in software manager Flatpak (brave) or command line install Flatpak (brave-browser).
I’ve tried uninstalling and reinstalling my Brave Flatpaks both through the Software Manager GUI in Linux Mint 21.1 and also via the Command Line Installer from the Brave Repository. Same problem.
Also see other users having the issue as mentioned here: