I have had this problem ever since I first started playing at the end of December. The mouse is only visible in W101 when it is moving, regardless whether I am in full screen mode or not. It is worst in battle at spell selection time, when I sometimes can't see it at all until I get it over the spell cards. I sometimes lose precious seconds desperately moving the mouse around trying to find it so I can select a spell! When there is a blotchy global spell like Balefrost over the battlefield it is next to impossible. My duel opponents often complain of the same thing.
In Control Panel of Windows, Under Mouse Settings, Pointer Options, there is a box you can check called "Show location of pointer when I press the control key." I have turned that on and it helps with W101; give it a try.
Sorry for the double post, but I just tried AloweArk's suggestion and changed the in-game option for Hardware Cursor from "off" to "on." This makes the mouse visible in the game even when it is not moving. :D