Godot windows appearing under main window

A strange issue that I'm experiencing in Godot 4.6 (this never happened in 4.5 or before), every engine button that opens a new window opens the window underneath the main one, even popup tooltips aren't showing up. At first I believed half of the engine buttons just weren't working, but after testing I could notice the window underneath, as demonstrated in the video. I can't minimise the main window, and this strange bug doesn't seem to happen using other games/software.

I'm using the Steam version of Godot 4.6 on Steam Deck desktop mode if this changes anything. I'm hoping the issue is me being an idiot rather than a bug, as Godot is completely unusable for me until a fix in that case. Please help!