After the huge upgrade that came down the pipe with Slackware, I got several irritating problems. I wrote about them here. One was a problem with Perl, but I eventually worked out how to fix that. The other one was a problem with X Window and how the mouse behaved. Positioning the mouse became problematic. I had to put the mouse cursor about a half inch to the right and a half inch below where I really wanted it. That got old really fast.
I had done the same upgrade on my Linux desktop at work, and it wasn't happening there. Different video cards, so can't really compare it. I searched through the LinuxQuestions.org forums, but no-one else had reported anything like that. It was up to me.
I looked at my xorg.conf and didn't see anything. But I experimented. After a few hours, I found the fix. I was using these modules:
Section "Module" Load "vnc" Load "glx" EndSection
I had installed them so long ago, that I cannot remember what they are for or what they do. I commented them out and restarted X and the mouse problem went away. I should have diligently tried each one to find out which of the two was causing the problem, but I had run out of patience and just wanted to get back to work. It hasn't caused any problems running without those modules.