Are you using epoxy resin or a urethane (like some of the Alumilite varieties and McKenzie Pen Works) resin?
My guess is you are using epoxy resin - which is VERY slow setting up, making it highly likely that the colors will blend.
You have to wait till they begin to get syrupy before pouring into a mold. With Alumilite and McKenzie's resin you can tell by the temperature, when they reach 95 or 100 degrees F they are setting and you can go ahead and pour in layers or swirl them a bit.
Each resin type has its own setting characteristics which makes "general advice" virtually useless. And beware advice about "Alumilite" without knowing exactly which Alumilite product they are talking about.