Ever since i bought the Wooting Two HE, I've been experiencing this problem and inspected the keyboards behavior before it occurs.
After setting my keyboard's effects (AOE), function layer included, the keyboard's effects will function correctly all the time. After rebooting the PC, the layers still function during the boot process until it gets to the Windows lock screen, where it seemingly stops working after numlock flickers for a split second and only shows my base layer, not producing any effects, not even for numlock/caps lock/scroll lock. This requires me to physically disconnect the keyboard every time my PC boots and re-applying profiles does not work until I re-plug the keyboard. I haven't personally tried resetting the keyboard due to it being a hassle with getting it set up again and resetting the keyboard that way every boot wouldn't be a fix on it's own either. My software is fully up to date according to wootility and I'm personally out of ideas.
I'm running Windows 11 Pro 21H2 and haven't tried the keyboard on any other computer thus far, I can also provide full PC specs or a recording if needed