If you have Scrollvetica running on your Mac from one logged-in account, and then you log in as another user, and run Scrollvetica from that account, then the swapping will be done twice - resulting in back where you started.
I suggest you check to see if the process with the Scrollvetica identifier is already running, and if so, don't do the inversion.
Fix for Issue #5: Only invert scroll events if our CGSession is active.
Dan, can you verify that this fixes your issue? (I'll tag and do another binary release once the fix has been verified.)