Jon,

You can use Edit Equipment on segments of pipe, and check the flow of each until you trace it back to the source. It could be something like an invisible drip area hatch, or an error with calculating the flow for an adjustable head. You can also use Highlight Station on each valve to check its flow, and to see if any large invisible hatches are highlighted.

—J

And if none of those work, you can remove pieces of the mainline to isolate the element causing the issue.