Alrighty. Since we know this isn't a problem on a fresh alternate account, then the problem is rooted somewhere in your user Library, or with something you are running in the background.
First thing to try is disabling everything that loads on startup.
Go to System Preferences > Accounts
Select your user and remove everything under login items. Then reboot and see what happens.
If the problem persists, then we need to figure out what it is in your user Library that is screwing things up. Go to ~/Library/Preferences and, after making backup copies, try deleting com.apple.finder.plist and com.apple.driver.AppleHIDMouse.plist. Then reboot and see what happens.
If the problem persists, then the only other thing to try right now is make a backup copy of the entire Preferences folder, then delete the original and reboot. This will reset your system and all apps to act as if freshly installed, but it will settle once and for all if the problem is a pref file, hidden or not.