I'm not sure that you can so-to-speak "fix" or better yet, disable the cursor to not show up. I'm assuming you are in Game Controller mode rather than Mouse/Keyboard mode from the configuration setting. When I play in game controller mode, the cursor will always appear when the mouse pad of the game controller is touched. I just simply touch the pad and move the cursor down and out of my way/view. After you click on any other button, the cursor disappears until your interaction with the mouse pad of the controller is done. It took me a while to get used to it, but now is no longer a bother. Just use the center pad of controller as your "PS3-version of Select" when you click on it, ensuring your cursor is out of the way (like the bottom of the screen), you may be less annoyed.

Not much of a here's-how-to-fix-it answer, but a band-aid solution.