I don't have my quad with me to see my numbers, but can you check in Librepilot:
Configuration tab > Input > Remote Control Input
With the Flight Controller connected to the computer via USB cable they "Channel Values" should change for Throttle, Roll, Pitch, and Yaw.
Are your maximums at (around) 2000?
Check the outputs also: Configuration tab > Output > Output:
Bank 1, 2, 3, and 4 should also be maxed at 2000 ish.
The other place to check is on the Hand-held remote itself. You can assign a given offset to each. Make sure they are not offset from the side buttons. There is a menu item that allows you to offset also. I'll have to wait until I have mine in my hands to see how to check it.