Whenever I open a program that uses gksu to give it root privileges it gets all flickery as it dims the background. Maybe this is just my problem, or maybe it's because of Beryl, I'm not sure. Doing the following will stop gksu from dimming the background altogether, it will just open a new window for you to put your password in.
Note: I am using Ubuntu 6.10, things may be different for you. I am not responsible if you screw anything up, but that would be pretty hard to do. You will not be modifying any vital system files or anything. This seems to be working really well so far, but I have been using it for all of 2 minutes. It's pretty easy:
Step 1: Code:
sudo mv /usr/bin/gksu /usr/bin/gksu_orig
Step 2: Code:
sudo gedit /usr/bin/gksu
Paste the following into the new file and save it:
Code:
#!/bin/bash
gksu_orig -g $@
Step 3: Code:
sudo chmod +x /usr/bin/gksu
And you're done.
Test it out by opening Synaptic, or putting 'gksu echo' or something into the terminal.
If for some reason you want to put it back, run:
Code:
sudo rm /usr/bin/gksu && mv /usr/bin/gksu_orig /usr/bin/gksu
Howto: Make gksu not flicker 
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