Try adding chloroform to better separate the aqueous and organic phase, lipids (other than glycolipids) will stay in the organic phase... just a guess.

I agree with Tausif chloroform or dichloromethane dosn't form an emulsion and the separation of the two fases occur without centrifugation. In any case a small centrifugation will help and accellerate the formation of two distinct fases.

What is the reason to treat your aqueous extract (AE) with diethylether (DEE) instead of any other solvent mixture? It is always useful to get at least a first idea of the different lipid classes present in your AE; moreover, the lipid composition of various plant organs (leaf, petals, roots…) can be quite different. If your goal is an extensive removal of all lipid classes – green pigments (CHL) & carotenoids (Car), phospho- & glycolipids (PL & GL), fatty acids (FA), sterols (St), acylglycerols (AG), etc – then DEE (which is a low polarity organic solvent) will certainly remove a good deal of non-polar lipids (CHL, Car, St, AG) but polar lipids (PL, GL) will be poorly extracted. The extraction efficiency of ionizable lipids also depends on the pH of the AE. This is particularly true for free FA, which are much more soluble in an aqueous medium when its pH < 4.

For the abovementioned goal, I would thus recommend a LLE method in which a mixture of two solvents is used. The blend is composed of 2 parts of the non-polar chloroform (or dichloromethane) and 1 part of the polar solvent methanol. The first is a very good lipid solvent of all classes. The second will help disrupting H-bonds between lipid headgroups and large polar molecules such as proteins. For the extraction, add 1 part of methanol and 2 parts of chloroform to 1 part of AE and shake strongly for 1 min. The synergic effect of this blend will result in a very efficient extraction of all lipid classes (don’t forget adjusting pH if required!). The emulsion formed upon mixing the blend with the AE is easily disrupted by a 5 min centrifugation (ideally in glass tubes with Teflon-lined screw-caps). Alternatively, larger volumes may be abandoned in large separation vessels. A nice advantage of the centrifugation step is that a solid “protein” cake forms at the interface between the upper aqueous phase and the lower organic phase. Usually, after repeating the extraction process once more, > 90% of all lipids will be removed from the AE.

Last remark: if you need to protect some water-soluble components of the AE from denaturation or oxidation, take appropriate steps (pH! N2 bubbling).