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I have the raspberry pi 2 with a hdmi - vga monitor running Raspian.
On programs like gimp and things I made in my game, my mouse keeps flickering if I move it across the screen, and if I don't move the mouse the pointer doesn't even show.
Open System Settings > Displays.
In the Displays window, you will see an Unknown monitor. Click it and disable it.
Thats a fix I used on Ubuntu when I had a similar issue.
Required, but never shown