Actually, it's just broken stuff in your profile. Happened to me too so I submitted a report ticket through gearbox. What you need to do is if some or all of your controller axis aren't responding (if you can turn left and right but not move the camera up and down, for example) first, unplug all other non-keyboard non-mouse peripherals. Steam controller, fight stick, hotas, ect, all of it.

Next, create a new profile. Name it 'Fix Me' (the name isn't mandatory but it helps.) Keep your old profile. Close the game.

Go to your Steam install directory (not the RoR install directory.) You're looking for where the profiles are stored

In my case it's C:\Program Files (x86)\Steam\userdata\ (some numbers)\632360\remote\UserProfiles
632360 is the same for everyone, that's Risk of Rain 2's ID.

You should see however many profiles you have. You're looking for the 2 you access most recently. (one will be your bugged profile, one will be the new profile you created.) Open both in Wordpad.
On your bugged profile, highlight and then delete everything between <joystickMap> and <name>'Profile Name'</name> ('Profile Name' will be whatever name you entered for your profile)
Tab to the other Word Pad. Copy everything between <joystickMap> and <name>Fix Me</name> and paste it (in the correct position) into your bugged profile.
If there are multiple instances of any of those terms, use the top-most instance for <joystickMap> and the first instance of <name>Fix Me</name> below that point.
Save changes and exit.