I can reproduce with that setup: I have two monitors with one on top of the 
other one:
VGA1 connected 1920x1080+0+0 (normal left inverted right x axis y axis) 510mm x 
287mm
LVDS1 connected primary 1366x768+0+1080 (normal left inverted right x axis y 
axis) 277mm x 156mm

The sync notification (like volume up and down)  is always overlapping
the top panel of the monitor with the focused window.

** Changed in: notify-osd (Ubuntu)
       Status: New => Triaged

** Changed in: notify-osd (Ubuntu)
   Importance: Undecided => Low

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https://bugs.launchpad.net/bugs/1292343

Title:
  notify-osd positions its top notification overlapping the panel on
  displays not aligned with the top of the virtual screen

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