I tried to extract chlorophyll from spinach by blending up some spinach and water and straining out the green juice, then heating the juice. I've done it before, but this time, it wouldn't separate. Does it not work if you overheat it? I brought it to the boil and I'm wondering if that was the problem.
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.