I've used the same 750mL of naphtha for a couple of KG of root bark and it has never turned black.  Yellow yes, orangish almost, yes, black, no.

It really does sound like an emulsion.  Heat it up, let it sit, tap the sides. If that doesn't work, take the black naphtha, add some water with a bit of lye (don't need much) and a bunch of table salt, heat, tap, wait.

That's the best advice I can give you with the info you provided.