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Are you sure you are doing it right? You need to click the Nexus, then the crafting altar, then flick the lever. Also try to check the Essence in the Nexus with a Magitech Staff, it might just be empty.
As a reminder, the nexus only will take essence when it requests it, and this only happens while crafting spells that require essence of some kind.
I've seen countless threads about this and all of 'em say "My Nexus won't take essence" and I'm getting tired of it.
Did those other 2 need light essence? Or are you saying with essence in the neutral nexus hooked to the crafting alter 1 spell will work then the next will not.