Here's what my /etc/X11/XF86Config-4 file looks like...
(The crucial line is the UseBios Option...
 because this gets rid of that nasty flickering)

Drive "savage"
Option "UseBios" "Off"
BusId "PCI:01:00:00"

it's for an
S3 ProSavage
running xfree86
driver 'savage'

if you don't have the savage
driver, it looks kinda like this...
get 's3savage-drive_1.1.23t...i386.deb' and dpkg -i it
  (or any newer version obviously)