I don't know if this is specific to QT, but since I was trying this with QT, posting here.
I am running Debian Trixie using Gnome as desktop
I downloaded fpcupdeluxe and installed v4.0 of lazarus with fpc 3.2.2. I loaded Lazarus, and chose to rebuild the IDE but with QT6 widgetset. I also tried downloading fpcupdeluxe qt version and installed the same (but fpcupdeluxe builds as qt instead of gtk when I use the qt version of fpcupdeluxe).
In both cases, when I startup the IDE, all windows are centered on the screen. I moved them to their correct locations for me (main ide on top, object inspector on left, messages on bottom and editor in middle). Closed the IDE and reopened, same thing. All windows centered.
Am I missing a setting somewhere? Does qt6 have issues with gnome and wayland? Not sure what is going on.