Testing different options I've switched ON "Use multi-row tabs" under User Interface > Options preferences - and this makes problem disappear, even if there's already mess in windows list. Don't know how displaying of tabs on top of the window can influence the "Window List", but maybe this will help you identify the reason.
Having this option enabled is also not good as a workaround for me...
False clue, only helped once, but after restarting switching this option doesn't help anymore...