The phenomena you observed, phase separation of your etchant, is not too rare -- sometimes, an ionic salt, water, and miscible organic "oil out", and phase separate like you observed. This will happen to my mobile phase for HPLC -- TEAA, water, and acetonitrile are all miscible with each other in a bottle, but sometimes separate, if allowed to sit inside a system, without a sizeable volume for natural convection to mix them. Your micro circits may even have more problems -- the hydrophobicity of the etched channel may draw the components apart ('tho that is just a guess on my part.) You may have to investigate surfactants compatible with your application.