I finally got the the extra universal serial bus device to go away altogether buy uninstalling it in the device manager about 4 times, restarting, and uninstalling another time and then pressing the program button on the back of the keyboard twice.
I thought all was well with my S60-x but it wasn't working right (one of the function buttons wasn't working correctly). I knew it must have something to do with that USB device listing, which shouldn't be there. Once I got it completely removed it works as intended. Now the only device that shows up there is the Atmega chip when I press the program button on the back. (before, even when the S60 was not in program mode it listed it as a USB device as well as an HID keyboard).
Friggin voodoo, but it's gone and everything works right now. I'm sure this is mostly specific to my setup, but I'm just keeping track of it here in case anyone could benefit. Aagain, I think this all happened because I was screwing around the zadig tool trying to be able to program a GH60 with Flip. Zadig is dangerous because you can force windows to run the wrong drivers. The good news is that a series of driver removals in the device manager seems to fix it.
TL;DR: Keep uninstalling drivers in the device manager (check box to remove all data) and eventually you can fix conflicts