I may have sent out a request for this some time ago, but now I can say
I've finally figured it out. This should work for most any setup where
you're using the mic on the front audio ports (so all Shuttle XPC's).

Mine uses the nForce2 chipset's onboard audio. I've installed ALSA,
which supports this chipset through the Intel i8x0 drivers. This system
has for sole microphone jack, the one on the front. All mixers I had
found were always only referring to a single mic port also. I finally
found somewhere that was stating that the mic should be set to MIC2
using amixer. I found another that stated that gamix was a very good GUI
mixer for ALSA. Turns out, gamix knew about "both" MIC inputs and let me
configure which one I wanted as the default. Set to MIC2, microphone now
works like a charm.

So if anyone's having issues with audio devices, and you're using ALSA,
give gamix a try.