Prevent application from changing the window layer

I'm running Debian 10 with fluxbox. I have an application where the window layer keeps changing to "Above dock", despite me checking "Remember..." "Layer". This layer change seems to happen randomly. How do I prevent this from happening? Pop ups created by the application launch with the "Normal" layer, so they are unclickable until I find them...certainly a very annoying issue. This *only* happens with this one application. Two more questions as asides: Do other window managers have this layer feature, or is it only fluxbox? What can control the window layer? Is it the window manager only, the application only, or both the window manager and application?