I've got two monitors, with the right side one being slightly lower in the display settings. However any notifications I receive from notify-osd (including pidgin, notify-send etc) are sent to the top-most part of the right monitor screen, which results it in being invisible.
And here's a pic of my monitor preferences :
I'd earlier used the Wallpaper plugin in compiz to stitch my desktops, and then uninstalled compiz-extras. I'm using Ubuntu 11.04 in classic mode.