Well I determined that the problem is that "Sparkling Dart" in the Alastor tree is not functioning properly. It isn't applying the damage bonus which is supposed to be 50% at max resource (and the numbers above seem to support that). I figured it out by checking my damage before and after unassigning the node and finding that there was no difference in damage shown. Also, "Static Transferral" in the Alastor tree is not functioning properly either. It isn't applying the 5% damage buff per stack, but I am not sure if it is still doubling the damage when stacks are consumed (but I am guessing it isn't). My guess is that if two major nodes in one tree are not working, then the entire tree is probably broken, but I can't be sure.

I just confirmed that the process of consuming stacks for Static Transferral does not double the damage of the skill.

Almost 1 1/2 years later and crucial skill nodes still don't work? Jesus Christ...