Some pipes don't get connected properly when wrenched down
When wrenching down some pipe types, they get wrenched down but don't actually connect to the other, nearby pipe.
All the thermal plates in this image are wrenched down, but only 1 layer gets cooled: http://i.imgur.com/uhf7NXe.png
From experimenting, I found that if you wrench the thermal plates down, THEN wrench the manifolds, the connections are made and cooling works properly.