Just tried toggling it on, then switching themes in fluxer and had no problems. Dunno if I need to like, reboot with the setting enabled or something but I can't do that atm.
Did you also try waiting for the Day-Night Cycle to take effect as well?
Because when it happened to me this time, the theme was changeable, but it required closing and reopening fluxer twice for the System theme to take effect
558003971-5153b6ad-c93e-42c4-b040-5ac055471bad.webm
Thread
Comment by @PlatinumLucario