Separating Chlorophyll didn't work
This author says to avoid overheating or boiling the green juice.  I suspect that your end product is actually clumps of chloroplasts not chlorophyll.  Overheating or boiling the chloroplasts could destroy their delicate membranes and allow the chlorophyll molecules to mix into the liquid.  It is not water soluble though, so you may be able to collect it using something like filter paper instead of a mesh strainer.  

Boiling can also lead to conversion of chlorophyll to phaeophytin, a olive-green pigment.