Comment 14 for bug 23917

I have the same problem but this will happen with either sudo or gksudo but NOT with all applications.
For example sudo gedit or gksudo gedit would trigger it but sudo synaptic or gksudo synaptic would work fine.
The same problem is present if you go and click something from System > Administration. Not everything triggers it. (In my case Users and Groups has a problem all the time).

After entering the password you are presented with a blank box that WILL eventually show but it can take some minutes.
The system is perfectly responsive during that time and the CPU usage is like 0%.

I did a clean install and I think this started since the beginning.