With no theme, Wanderer windows end up not backfilling. That's a bug, but kinda expected since Wanderer sets LAYERS_NOBACKFILL on all windows:

[OpenWindow] 'RAM Disk:' backfill LAYERS_NOBACKFILL (0x00000001) flags 0x2024127f

But I don't understand why CON: windows would also look transparent with the default backfill hook:

[OpenWindow] 'AROS-Shell' backfill LAYERS_BACKFILL (0x00000000) flags 0x2804101f

I suspect it only happens with P96 card drivers... and only after IPrefs has run.

I've had similar problems and for me the problem was that the background images were "just" not reachable and adding the right X: assign solved the problem.

I fixed this finally: github.com/aros-development-team/AROS/pull/961

Better to have the correct fix thzn working around it like me. Well done.