Comment 13 for bug 475373

I have a similar problem, I think. With two monitors, a 1280x1024 LCD above my Acer 3810T laptop's 1366x768, my notifications are only partially on the upper screen (improperly right-aligned). Thus I can only see the first part of any sentence popping up from pidgin, etc. Works fine with no external.

$ xrandr -q
Screen 0: minimum 320 x 200, current 1366 x 1792, maximum 8192 x 8192
VGA1 connected 1280x1024+0+0 (normal left inverted right x axis y axis) 376mm x 301mm
...
LVDS1 connected 1366x768+0+1024 (normal left inverted right x axis y axis) 293mm x 164mm

$ /usr/lib/notify-osd/notify-osd --debug
** (notify-osd:22729): DEBUG: selecting monitor 0 at (0,0) - 1280x1024
** (notify-osd:22729): DEBUG: no panel detetected; using workarea fallback
** (notify-osd:22729): DEBUG: top corner at: 1031, 22

notify-osd is pretty but has a been a royal pain in the ass due to lack of any straightforward configurability.