That was quick, b-boy. You had your problem more than four years ago and yet it still persists? As I said, I don't think a preference file is affecting it. I booted from two different partitions and the problem was across both, using different sets of system files.
Just before typing this answer, it happened again! That's twice in two days. I removed the mouse's receiver dongle from the USB port, replaced it and the Dock returned properly. I'm starting to think that maybe my mouse battery is running down because I never switch it off. I'm using 10.4.8 and a Logitech mouse, which, by the way, scrolls sideways, too.