So when pointer disappears how do you navigate, does it come back when you move the mouse?
Have you tried installing a different mouse to see if its a mouse issue? Have you scanned for virus's and come up clean?
Does anyone else have access to this system that may be trying to annoy you with a program running on this computer that hides the pointer to a far corner of screen and you lose mouse controls? (There use to be a very annoying program to install to a friends computer called Drunk Mouse which made mouse controls offset and laggy, and so thats why I am asking if anyone planted anything on your system to play with you and frustrate you. These sort of programs exist to annoy. )
Aliases of Drunk.Mouse (AKA):
[Kaspersky] not-virus:Joke.Win32.MovingMouse
http://www.exterminate-it.com/malpedia/remove-drunk-mouse