It seems this happens when composite is on and the option 'Display shadows under popup windows'is turned on, leave that option unchecked and it works as it should, one user in above mentioned thread also noticed replacing gksudo with gksudo -g worked.
It seems this happens when composite is on and the option 'Display shadows under popup windows'is turned on, leave that option unchecked and it works as it should, one user in above mentioned thread also noticed replacing gksudo with gksudo -g worked.