The latest unstable release of the game (on the previously mentioned unstable branch) has a new input manager implemented. This has allowed input configuration to be made much more streamlined, with axes and buttons being interchangable and support for future splitscreen being easily achieveable now too.
If you've been having issues with inputs (Xbox One controllers on Windows 10 for example) then definietly give this update a go as it could potential fix problems such as those.
If you've been having problems and try out this update, let me know how it goes in the comments on this announcement.
Have fun!