Do you have the x360ce program, ini file and xinput1_3.dll file it creates in the EE shipping install folder?
In the Game Settings tab, on the My Game Settings tab, there are checkboxes to specify which xinput files to use.

https://github.com/x360ce/x360ce

I only tried x360ce briefly to get a Steelseries 3GC working, but it didn't recognize the sticks, and I didn't do much troubleshooting. I had it set up and fully working using motion In Joy, but it stopped recognizing the controller at all, until I went through the initial setup again. It also wasn't recognizing the sticks properly, but I couldn't remember how I set it up the first time (I didn't have to do anything special).
The problem was rendered moot by a sale on a better controller.