At this point with current kernel gksu is pretty much broken.
An initial bug report is here, currently marked incomplete though that should change (or I'll change or dupe
In cases where pkexec is usable it can be set up & used instead (text editors, file managers
or ( and in the case of gdebi which is gksu only
Remove ~/.gksu.lock prior to attempting to use gksu (must be removed for each use of gksu
*Not recommended* - disable the grab mode in gksu-properties for Screen grabbing
Even when working there seems to also be cursor run on which is not particulary a good thing so where applicable I'd switch to pkexec until this is fixed