Why does input seem to be handled differently in Game View vs an actual build?

I am attempting to use both thumb sticks on a generic usb controller. I wish to use the left stick for the player object, and the right stick for the camera position. After several hours of fiddling with Input Manager (yes I am quite new to Unity), I finally managed to get the controls to work properly in a build of the game (building to PC, Mac, Linux). However, in the game view (testing the game within Unity), the vertical axis on the left stick overlaps the vertical axis on the right stick. In other words, while testing the game within the Unity Editor, the left stick controls the vertical camera AND the vertical player movement. In the build, however, both sticks work correctly.

When starting the build version of the game, the 'game launcher input window' appears and allows me to configure the controller before beginning game play. How can I 'lock' this configuration so that I can test the game in the editor correctly?