HDA audio has a unique "feature" called "jack sensing" (jack in this case is not jackd) where it changes how the audio interface is laid out by what it senses you have plugged in. This allows the MB to have fewer HW jacks while still having lots of i/o. there is an application called HDAJackRetask that _may_ help. Be aware that plugging and unplugging things will change how things are set up. Dirty contacts may effect things too.