I am running Centos 4.4 on an SMP x86_64 system with kernel 2.6.19-mm1 compiled from kernel.org. I recently tried to upgrade to kernel 2.6.20 due to an issue with reiser4 and after booting with the new kernel my PS/2 mouse would not work under X. The strange thing is that it works fine in the console. If I move the mouse, I see the cursor moving around on the screen. I tried changing the xorg.conf but that doesn't seem to change anything. Booting back with 2.6.19 fixes the problem. Everything in /dev and /dev/input looks the same between the two kernels, and I built the 2.6.20 kernel by copying the .config file from the 2.6.19 source dir to the 2.6.20 source dir.

Any ideas what could have changed to break the mouse in X?

Here's the relevant section of my xorg.conf:

Section "InputDevice"
Identifier "Mouse0"
Driver "mouse"
Option "Protocol" "auto"
Option "Device" "/dev/input/mice"
Option "ZAxisMapping" "4 5"
Option "Emulate3Buttons" "yes"
EndSection

Try sudo dpkg-reconfigure xserver-xorg. It is actually a graphical type of setup for your xorg file. It takes you through monitor and resolution settings as well as keyboard and mouse.

dpkg-reconfigure is a debian command. I'm running Centos and don't have that particular command available to me. I have, however, run through the Centos equivalent to no avail.