I also have this problem (which is very annoying since I am working on a RandR applet ;). Every time I switch the mode of the current output, (e.g. from 1024x768 to 1280x1024), the icons keep floating at their old position (in the middle of the desktop) and are only redrawn in the correct place when something changes in their composition (e.g. a new task appears).
Ubuntu Hardy, awn from bzr, using AWNLib.