As stated in the description, The alsamixer's master does absolutely nothing, while the headphone and PCM seem to control all sounds coming from my speakers. There are only 3 audio jacks in this computer, line in/out, microphone, and speaker (or headphones will fit). Is there any specific reason for this?

It doesnt bother me that much, as Xfce's mixer has headphone maxed out, while controlling the PCM, which works ok...