This is a problem with Hildon-Desktop. It turns out that when you return to the desktop from a non-minimized window using the task switcher menu on the bottom left of the screen, that Hildon doesn't minimize the window, it takes a quick-and-dirty shortcut and only shoves it "behind" the desktop. This normally has the same effect as minimizing the window, but when the desktop is transparent, you can see right through to Hildon's little cheats. So this effect only happens if you leave the application's window open; if you minimize the application windows, they don't "show through" the desktop. You have two choices; you either see the X root window through a transparent desktop, and then you also get this side-effect, or you kill the transparent desktop and get neither X root window nor open "background" windows.