I am running Xubuntu 12.04 on a Macbook 2.1 intel duo. But the problem existed on Ubuntu 12.04 too.
After booting up, the internal microphone doesn't work. After opening the Pulse Audio settings and changing the configuration, it will work after. However after suspending or shutting down, the microphone will not work again until changing the configuration again, even though the actual config didn't change.
Right now I have to always switch between the Anglog Stereo Duplex and the Analog Surround 4.0... each time. Is there anyway to get this microphone issue fixed? It seems like a problem with Pulse Audio.