So I have 2 bearded dragons, and one of them recently started running around it's cage, with its beard black, and repeatedly bobbing its head. It stops for a while, and then does it again. My other bearded dragon, however, is acting completely normal. Any reason behind this?
Totally normal.
What you're witnessing is your little black beardie establishing dominance. Their beards will generally turn jet black, and they may scurry around a bit, bobbing their heads. Males will often do this as a sign of courtship too, while a female beardie will do a 'waving' motion with her arm, which is also known as a submissive gesture.
How old are your little ones? And as long as the bobbing beardie isn't being aggressive/harming the other, it should be just fine.