I am experiencing what is probably the same problem. nvidia-glx-config
enable made the following changes:

--- xorg.conf   2006-08-11 17:13:25.000000000 -0400
+++ /etc/X11/xorg.conf  2006-08-11 17:13:40.000000000 -0400
@@ -99,46 +99,46 @@
 EndSection
 
 Section "Device"
-       Identifier      "NVIDIA Corporation NV17 [GeForce4 420 Mac 32M/GeForce 
440 Go 64M]"
-       Driver          "nv"
-       BusID           "PCI:1:0:0"
+       Identifier      "Generic Video Card"
+       Driver          "nvidia"
+       BusID           "PCI:0:5:0"
 EndSection
 
 Section "Monitor"
        Identifier      "Generic Monitor"
        Option          "DPMS"
-       HorizSync       28-64
+       HorizSync       28-51
        VertRefresh     43-60
 EndSection
 
 Section "Screen"
        Identifier      "Default Screen"
-       Device          "NVIDIA Corporation NV17 [GeForce4 420 Mac 32M/GeForce 
440 Go 64M]"
+       Device          "Generic Video Card"
        Monitor         "Generic Monitor"
-       DefaultDepth    16
+       DefaultDepth    24
        SubSection "Display"
                Depth           1
-               Modes           "1280x800"
+               Modes           "1024x768" "800x600" "640x480"
        EndSubSection
        SubSection "Display"
                Depth           4
-               Modes           "1280x800"
+               Modes           "1024x768" "800x600" "640x480"
        EndSubSection
        SubSection "Display"
                Depth           8
-               Modes           "1280x800"
+               Modes           "1024x768" "800x600" "640x480"
        EndSubSection
        SubSection "Display"
                Depth           15
-               Modes           "1280x800"
+               Modes           "1024x768" "800x600" "640x480"
        EndSubSection
        SubSection "Display"
                Depth           16
-               Modes           "1280x800"
+               Modes           "1024x768" "800x600" "640x480"
        EndSubSection
        SubSection "Display"
                Depth           24
-               Modes           "1280x800"
+               Modes           "1024x768" "800x600" "640x480"
        EndSubSection
 EndSection


This shows the same bus ID change that others have mentioned, but also shows a 
change to the monitor config (a bit scary this should physically damage old 
monitors) and to the modes (a big problem on a wide screen laptop).

I am using Edgy (updated today) i386 on a Compaq R3000z.

-- 
Running nvidia-glx-config enable breaks X.
https://launchpad.net/bugs/48077

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