I have an application that sets itself to "always on top" somehow, but when I right click on the title bar, the "Always on top" option is grey. Any idea what could be causing this? The application is using SDL for the window in question, but has some additional Xlib code. I have access to the source code, but don't know what exactly to search for. Any ideas?
I found out what it is. The "Always on top" option is enabled only if the application is in either the "normal" or "above" layers (as per wmctrl). Put it in any other position (below for example) and although the window manager respects that on my desktop (and doesn't on a custom built machine), the "Always on top" option is grayed out.