OK This is really a non-answer but there is too much information for a comment and iut may be the only answer.
First here is a bug report for this
https://bugs.launchpad.net/ubuntu/+source/unity/+bug/894348
However there is no fix
Heres some info I found Why don't applications opened as root use global menu?
For an application to use the global menu the environment variable $UBUNTU_MENUPROXY needs to be set to to the name of the menuproxy library to be used. For security reasons this variable is cleared when using sudo etc. to run a program as root.
As a side effect this indicates which programs are run as root, otherwise it may be not always clear that the items in the global menu belong to a program running as root.
As this are good reasons for the current behaviour I don't expect it to be changed.
This is really all I could find on this, to give a short answer
There is no fix this seems to be related to security in Ubuntu and root, there will probably never be a fix.
However if it really annoys you, you can remove the global menu (task bare menues) and put them on the windows for all users, like this
sudo apt-get remove indicator-appmenu
And put it back like this
sudo apt-get install indicator-appmenu
If you just want to remove it for the certain apps please review this http://www.webupd8.org/2013/11/unity-global-menu-can-now-be-disabled.html