Sadly Game Maker is far from perfect when it comes to mouse management...
You could try going to open settings.ini in "C:\Users\XXX\AppData\Local\BE_Witches", where XXX is your username. Set mouseYCalibration and mouseXCalibration to 0, hopefully that will help but I can't guarantee it!
I'll be posting a new build on December 1st which fixes that issue, but it also introduces a different cursor bug for some people... Kind of a whole story but basically I have imperfect workarounds for that new one, and I'm waiting for the Game Maker engine itself to receive an actual permanent fix.
But yeah, in short if settings.ini doesn't work you might simply want to wait for the new December 1st version! ^^