ya it will happen after a storage of about more than 6-8 hrs. So in your case when its happened....? the phase separation is just because of addition of higher volume of continuous medium....
what's your continuous and dispersed medium ratio used initially to prepare the NP? What about the initial emulsion stability/ nanoparticle formation......? Just try without the addition of water....i.e instead of that wait for the solvents to diffuse out and evaporate...or..try the process in little high temperature than what you have tried.
I found my problem...... I'm using a protein as a cationic agent and also, I'm using chloroform and acetone as a organic solvent for the polymer.. this is my problem :/