I have this exact same issue, but found a post at:
http://ubuntuforums.org/archive/index.php/t-1139434.html

that explains that you now must hold down the ALT key when you drag a
panel from one screen to another.  I did that and it resolved my issue.
I was able to move the top panel to the primary monitor (the bottom
panel was already showing on the primary monitor) and it persists this
change after a reboot.

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only top gnome panel moves to secondary monitor on metamode change
https://bugs.launchpad.net/bugs/360619
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