This really needs to be addressed. I think Preston's fix would be most ideal since there's no legitimate reason for placing more than one of an item in the ingredient slot.
I had built a multi-stand brewing machine during the snapshots, and just returned to it today only to find that this fix broke it completely. The only workaround I can think of would vastly increase the complexity of the control circuits.
Just confirming, this is definitely not fixed in 1.6.2. I loaded a fortress that was generated in 1.5.2 and the fortress-only mobs are only spawning in the few areas that overlap with the 1.6 version of the fortress; which is the same behavior as in 1.6.1.