We had a good tournament, only losing once in pool play (to a lower ranked team) and we even won the tournament. But, our points actually went down at the conclusion of tournament while the second place team jumped a bunch. Why?

The absolute key thing to remember is that the points are a "relative ranking". Please note that in this system, winning does NOT necessarily equal points going up and losing equals points going down. Instead, winning and losing should change the differences in points rankings between teams that play each other. In this example, the second place team may have gained a lot of points to draw closer to the winning team (whose points may have gone down as result of their one set loss to a lesser ranked team). The idea is that these changes are expected as the two team’s rankings are supposed to draw closer together since a lower ranked team beat a higher ranked team.