I notice when I open new windows (like Photos), the overlay doesn't stay on top. If I click on a photo in file explorer, it opens in Photos and is uncensored. I have to click on the overlay window again to put the censor back in place. This is with "prevent the overlay to be minimized" checked. It also sometimes causes the overlay to disappear if I click on the screen while in Photos, and I have to select the overlay window again.

Anyone have any fixes or ways to stop this from happening?

Indeed, I have the same thing if I use the Photos app from Microsoft. This seems to be a problem from Photos, which bypass the fact that the overlay should always be the topmost window. Do you experience this with other applications ?

Even using the Always on top PowerToys from Microsoft didn't solve this. 

For now, the best fix I see is to install and use the Legacy Photos from Microsoft which doesn't have this problem and mostly looks the same. XnView is also a very good image viewer.

I do have the same issue, with both Photos and MPV video player - but only when mpv is set as default program