To replicate the issue this is what i did.
I created a new TouchInterface and configured it to only have 1 thumbstick situated on the right. Controlling Gamepad RightX and RightY.
My input config is set to use those values as the LookupRate and TurnRate under AxisMappings.
I then have an event for those inputs.
When a left thumbstick is present that is configured for Gamepad Left X or Y values, then the rightX and Y values work correctly.
However due to only using the right thumbstick the values are somehow overwritten to interepret it as the Left X and Y values.