you logged out when you are doing this? config file will revert if it's being used by the program already. need to be fully logged out of ryzom and the program closed, then make the change. Then log back in. Before starting the second client.
I do recommend having ryzom in two different directories for this. Just for the fact that it does save config files when you log out, so if you do like to have one set up to have max graphics, and another set up to min graphics default and not having to change it each time you login

. Also have noticed occasional bugs associated with 2 clients running off the same directory. Usually when I do this, one of the clients will pop up that message you get as your logging out, the skill points thing, then render my character unable to move, and it will crash shortly later. Doesn't happen immediately or consistently, just sometimes.