i am having the same problem. i already looked at xorg.conf, the x config file, as suggested, and i don't think that's the problem. In my case, i have found that if i log out of x, and switch to root with su, and run "/etc/rc.d/rc.hotplug restart" the mouse will work when i start x again.
i just read five minutes ago, and already i forget where, something about hotplug and that cold plug devices such as mice are a somewhat special case, because some of the modules needed may not be available at boot time when they are first detected and so hotplug must some how rescan the mouse later on in order for it to work.
i don't know why, but it used to work until i started messing around to get acpi to work, which is a long story. So what I'm leaning towards as a solution, is exactly what hotplug configurations should look like across all of my startup files, what permissions and paths are involved, etc. I don't know what is different now than before unfortunately, but adding "/etc/rc.d/rc.hotplug restart" to the startup might be an easy fix but it's going to really slow things down.
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