My temporary solution is to simply ignore the any additional instances of the program and focus on a specific window (by bringing up the window I want). This way, it will show and hide that window until I accidentally bring up the other window, which then just means I'll have to restart the app.
Although another minor issue would be how in order to perform the macro on the specific window, I lose focus on say my web-browser and I have to click it again just to resume work.
But I guess that can't be helped, since it only detects keystrokes on the window it's currently focused on.