It seems as though you have the JomSocial Facebook features enabled. These don't work with JFBConnect as they both are attempting to do the same thing and include very similar code into the page. This can confuse Facebook, which they don't like.
Try disabling the Facebook features in JomSocial. If that doesn't work, can you provide a specific page that doesn't work and if there's an error that you see, a button that's missing, or whatever is 'not working'.