I'm in the same boat. When I first installed, everything was great - only the Cursor FX cursor, but after I rebooted, now I get the dual cursors. I'm running Windows 10 ver 1803 and Cursor FX is 2.16.
The bat file uninstalls, but after I re-install, the problem comes back.
Yeah, the bat file doesn't do squat. It's some sort of bug in the code that doesn't refresh the cursor change. I get it at random times, like when I add/remove a monitor or something resizes my window like the Windows smartscreen or a game that runs a different resolution than my native desktop res.
What I usually do is just go back to the Windows default cursor and then change back to the custom after a reboot or shutdown. Sometimes it works as intended and sometimes not. I wish I had access to the source code since Stardock seems to have no desire to look into the problem.