Liquid not pumping at all when one of two pipes in a junction blocked

Is that pipe going through your valve in the top left?  like THROUGH?  Thats causing a pressure confusion in your line, rebuild either inlet pipe on that valve and you should be good to go

It was actually. If that's what was causing it, then I think it could be related to this attached issue (which is caused by pipes going through objects they shouldn't be going through).

 

Indeed, on the filter, deconstruct the central section of pipe(orange) connecting it only to the right hand outlet, that should fix that one.

Edited December 30, 2017 by Kabrute