I'd say definitely don't rule RI out yet, it's possible that it's just in the beginning stages, you never know. However, it is also quite possible that the combination of both being housed communally and in such a large enclosure (although I understand that's the best way to go if you must house communally, don't change it) could be causing stress, and I've heard balls make that stress noise quite a few times. It sounds almost like a cricket chirping sort of, right? It could just be that the snake is stressed so he's making that noise.
Again, keep an eye out for RI's anyways, and if the noise stops after the separation then you'll know that's probably all it was -- stress.