Have you gone to 'Run Program' and clicked on 'refresh' when both controllers are attached? Then you should see each one operating independently.
When you define buttons using 'Configure Robot Action', just keep an eye on whick controller number is specified.
When you 'prototype' or 'generate code', the 2 controllers should work as defined.
Additional troubleshooting suggestions:
- Make sure the switch on the bottom of each controller is in 'D' position
- Swap the controllers in the USB ports you are using (bad controller? bad USB port?)
- Clean out the 'Human Interface Devices' in your 'device manager' that appear to be the controllers, and start fresh [last resort]
These approaches are what we've found useful when confronted with 'controller problems'