Hey Jon!
I am sorry to hear about the issues you have been having. For this type of situation, the Display Setup Tool can be really handy. Below is a link to download this Display Setup Tool. Then, you will run it with MediaShout CLOSED to set the screens correctly before launch. Then, when you open MediaShout, everything should open correctly.
https://support.mediashout.com/556638-Display-Setup-Tool-for-MediaShout-6
Please let me know if you continue to have trouble with this.
Thanks,
-Ryan