Unfortunately the settings window is still bugged. I looked into it and it must be a bug in SDL2 because there's no reason the scancodes for those keys shouldn't be read in properly by the library. However, I was still able to bind the Right Shift and Right Ctrl keys manually by editing the default.cfg file generated by the game and inserting the correct scancodes for those keys there. So here's a short list of scancodes for those keys and a few others that are also apparently not behaving right:
I got those numbers by referencing one of SDL2's header files which you can see here: http://www.libsdl.org/tmp/SDL/include/SDL_scancode.h
simply insert those numbers into any of the lines that start with the /bind command in your default.cfg to rebind that key. You only have to do this once, the game will retain those settings forever.
Hope that helps :)
Thanks, if you haven't yet you should try this little game that uses this concept (free download):
Of course Barony is totally different, but I like how gaining health with exploration adds strategy.