I have the same problem.  I have a Radeon 3850.  One 19' 1440x900 LCD,
and one 19' 1152x864 CRT.  The GNOME panels are on the LCD, so I suppose
that's the primary.  I started with the ati driver, which works
perfectly.  Using the Preferences --> Display applet, I de-mirrored the
displays, and set the above resolutions.  I then switched to fglrx using
Jockey.  The resolutions carried over.

With fglrx active:  GDM is mirrored.  While loading into GNOME, the
loading process takes quite a bit longer that when using the ati driver,
and the CRT flickers repeatedly.  As soon as the panels load, the
flickering stops, and the panel contents then load quite quickly.

When I start the Display applet, I run into the same flicker+slow X+grey
square problem as above.  The only way out of the situation is to log
out, which takes a while, as the panels are fairly unresponsive.

I also get the flickering when just loading up Totem, but strangely, not
Banshee.  When playing videos, the audio is fine, but the video is quite
choppy.  I've tried opengl overlay with video overlay off, and I've also
tried opengl on + textured video on.  I've tried adding these options
with both aticonfig, and just manually, with gedit.

I don't know if this is relevant, but with fglrx and compiz active,
windows maximize across both monitors, rather than just one.  Also,
maximizing takes about 2 seconds.  Minimizing is a fraction of a second,
as usual.

With fglrx active, glxinfo reports direct rendering active, and glxgears
gets ~10000 fps.

I've switched back to the ati driver, because a working desktop is more
important to me than a pretty one :), but I'm happy to switch back to
try things out, if anyone has any ideas, or wants more information.
I'll be keeping an eye on this page.

Thanks for your time,
Ryder

-- 
Xorg high processor usage and flickering screen with fglx/dual screens
https://bugs.launchpad.net/bugs/365311
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