I also don't have any trouble getting brown rice cooked right in our rice cooker/steamer. But I tend to cook it much longer than it is supposed to take and I use a little less water than suggested.
I have also noticed that Chipotle Mexican Grill has started offering brown rice and when I get it, it is pretty awful because it is not cooked right.
I am not sure of the chemistry/physics but I wonder if brown rice is much more sensitive to storage conditions, altitude, or something similar. I can't imagine that Chipotle did not test their cooking recipe thoroughly at some central test kitchen. But whatever they are doing in the restaurants near me is not working! Their white rice though is always perfect. Anyway, maybe that could explain why your cooker is not doing it right.
Why not just experiment yourself until you find the combination of rice, water, cooking time, and holding time that works for you?