Resolved an issue with my keyboard causing one device, not always the same device, to be inaccessible to the windows setup usb controllers app. Got a different brand keyboard. I'm not convinced that was causing my two Arduinos to become mixed up by other programs though. I did find a solution for that. Using the Arduino IDE I changed the board type from Arduino Leonardo to Arduino Micro for one of them. Works perfectly.
I also bought an Arduino Mega R3 knockoff which has as much or more functionality than the two Leonardos combined. I'll probably get around to making a new box with more functions. Eventually.