By all means I can't think of a reason the skinning would be an issue, but I don't know enough about the Atari ST terp to be certain. LB1 had skinned windows, even in its Atari release, but done in a different way, so...
Either something is wrong somewhere in the input handling, or something is fishy about window drawing. The game seems to load rooms, but have you tried to open any other kind of window, through the menu? If something like the About window also crashes...
(Edit: the LB1 windows are done
the same way KQ5's are, with lines for the edges and drawcel calls for the corners. Not exactly how Brian's code does it, nor like Sierra's BorderWindow in SCI1.)