Each time I quit atril and restart it on the same document, the position of the window is moved 4 pixels rightward and 28 pixels downward. This seems to correspond to the size of the window decorations (borders and title) set up with my window manager (FVWM).
Actually, the problem is more with restoring. Note that a consequence is that the window may appear partly off-screen (this was how I noticed this issue), which is annoying.