Another problem I had with my Slackware 9.1 system after running xf86config was that it seemed to doing things 'behind my back' after having configured X.
Once I'd configured the XF86Config file I ran startx (I think it was) and up popped my xfce for root (I was still root), great I thought, all is well.
However when I rebooted, something somewhere had configured xdm to work for local as well as remote connections. This was (sort of) OK but I'd really prefer it not to happen in the future as:-
Most of the time I run my Linux desktop on my WIn2k system using an X server. If/when I log into the Linux box directly it's because something is awry and very often running X automatically will simply get in the way. I want to default to a command line login locally.
It uses resources unnecessarily
How do you shut down? In the end I CTRL/ALT/F2ed to an alternative console and ran 'shutdown -h now' there but this seems a bit convoluted and as it's not the system console the messages get a bit confused.
It meant my mouse problems were worse because gpm had got the mouse configured wrong before X got a look in (or something like that, I haven't really sorted it out yet).