If you are hitting the save setup button after you enter your channel config the only time I get that message is when I mess up a channel number in my models. Last time I had that happen I was experimenting with different matrix configs and did not pay attention to the ending number of a large matrix. I would guess you added a model that caused you exceed your network config and I don't think that is checked except when you start the program so you could add a model that went beyond your config and you won't get an error until you close and reopen nutcracker.