Controller controlling more than 1 instance

[Wrinked4Skin]

I have been using NucleusCoop fine for months now. I play KB+M, my girlfriend uses a DS4 controller with DS4Windows.

I recently attempted to use X360CE for Saints Row 3, because DS4Windows was not working for that game. And then boom, everything stopped working. Now when I load in to any game, her controller controls both of our instances. I can still move around on my KB+M instance, but her movements are added on to mine.

I've tried deleting X360CE. I am not sure if it created files hidden in some directory? Or changed any controller settings/drivers?
I read the FAQ up and down and have been troubleshooting for hours on hours. I tried exclusive mode for DS4Windows, disabled steam controller, uninstalled/reinstalled multiple versions of DS4Windows and NucleusCoop, but nothing seems to work. I am wondering if there are DLL files from X360CE laying around somewhere on my machine that interfere with Nucleus's functionality. I have tried booting the game up and pressing buttons on each input device in every combination you can think of. The only games that work are ones where I can disable gamepad on the KB+M instance (which has only been l4d2 at this point). Any help would be appreciated. I am at my wits end, seriously about to do a clean reinstall of Windows to get this working again.

Also, let me sneak in a quick "thank you" to the developers of this program. My girlfriend and I have had many hours of fun using Nucleus. I hope more recognition is spread to you guys & your project.