al_get_window_position(...) returns the client rectangle x and y coordinates and not the actual window coordinates.When you do following to window with borders:
al_get_window_position(display, &x, &y);
al_set_window_position(display, x, y);
You will notice that it moves.
It also happens with frameless windows when you run the program in a sandbox (tried avast! Free Antivirus autosandboxing).I only tested it on Windows with allegro 5.0.7 so I don't know if the same behavior applies to Linux and Mac.
I believe this is fixed in git as of revision 31ba84f.