Did you add the commands to both the Input\Joystick\Default.lua and Input\Keyboard\Default.lua? From your description it sounds like you've added them to only one of them.
Anyway, in today's "I really can't believe they left out this command" segment: Separate up and down keys for the landing gear in the P-51D/TF-51D.
Working perfectly:
{down = device_commands.Button_3, cockpit_device_id = devices.CONTROL_SYSTEM, value_down = 1.0, name = 'Gear Up', category = 'Systems'},
{down = device_commands.Button_3, cockpit_device_id = devices.CONTROL_SYSTEM, value_down = -1.0, name = 'Gear Down', category = 'Systems'},