Comment 4 for bug 763579

Does Monitor Preferences show multiple outputs are turned on? If so, this could easily be caused by bug 815454 which would render the shadow for all outputs only on the top output. So you could get multiple overlapping shadows.

Another cause of multiple overlapping panel shadows is having multiple panel windows. Even though you often will only see one panel, their shadows will overlap and look really dark. That is bug 769957 - a window leak in the nux library causes multiple shadows to be rendered. And only one would render correctly, so the others might overdraw other windows.