Discontinuous Flow in Flow Simuation

Hello all,

I am trying to simulate flow through a hydraulic press system. For some reason the flow subdomain becomes discontinuous after a short period (first image). Strangely, if i make the section shorter, the flow reaches to the rest of the system but there is still a strange excluded section in the flow. I have tried redoing the routing, using a swept path and having a different origin point for the route but nothing I do fixes my issue. 

The other sections have no issues and they seem identical to this one, any help would be greatly appreciated.

Apologies for the low quality images, there is a green line slightly outlining the section and a blue arrow pointing to it.