Empty Pipes block flow.

I cant tell from your screens because they dont show the whole net. But usually its not a problem with the content, but with the design of the network. If the content can flow to different exit points the system will back up. Use bridges to make clear in which direction the content should flow.

Used bridges and had the same effect. attached picture of an expanded view of the current problem. Didn't have this issue on this playthrough until the recent change to the pipes. 

Avoid T-junctions when you have multiple inputs and outputs in the same pipe section. It behaves funky sometimes.