Dr. Poe,
Dare I say it - "you haven't provided enough information to effectively diagnose this problem."
So, I will speculate instead.
First, liquid/liquid separation problems are extremely common in industrial liquid ion exchange ("solvent extraction"). Along with sludges precipitating in the settler, they are probably the most common problems in industry.
Some thoughts:
1. you don't specify diluent. While doing shake-outs in a sep funnel may not require diluent, most SX processes use diluents for a wide variety of technical reasons, including improving separation. Kerosene is the most common diluent.
2. phase modifiers are also very common. The higher alcohols, like decanol, are very common to reduce organic viscosity and improve separation.
3. other species in solution may be poisoning the organic. The most common (for sep problems) is silicic acid, formed by weak acid attack on silica and silicates at some stage in the process. These act like emulsifiers and form a snotty-looking mess.
4. you didn't specify equipment used. If they are using mixer-settlers, overly vigorous mixing can often create an emulsion which is very difficult to break, especially given the limited amount of time typically available in the settler. There is sometimes a fine line between "overly vigorous" and "insufficient" when it comes to mixing. Also, some systems really require "picket fences" in the settlers to assist in breaking the organic/aqueous interface. If they are using columns, then again agitation can play a role - for example, in air-mixed columns, sometimes the air bubbles are too fine and produce local areas of frothy emulsion that is later very difficult to break. I don't have an isotherm for your ethyl acetate/gold system, so I cannot comment on what might be the most appropriate contact system to begin with...
5. acid control - generally this is carefully done in the lab and sometimes completely absent in the plant. Most organic/aqueous systems have ideal acid levels not just for extraction efficiency but also for physical properties. In particular, I have seen quite a few problems when extraction was allowed to become too acidic (since usually the organic is giving off hydronium ions in exchange for the metal ion complex) followed by too weak acid stripping - not only does the extraction efficiency suffer, but often the organic goes either too "thin" or more often too "thick" (making emulsions easier to form).
6. temperature control - it should be obvious, but a lot of organics become more viscous as the temperature declines. They might be running their plant too cold compared to lab conditions.
7. organic degradation - exposure to too much acid can cause the organic to degrade. Degradation products usually make things worse. I don't know how stable ethyl acetone is (but based on the ethyl and the acetone parts, it won't be very stable compared to robust organic extractants like D2EHPA).
8. oil leaks - I have seen this once - an auto-oiled mixer was leaking thick oil/grease into the system, causing all kinds of havoc. Best found by walking around and looking.
I am sure there are other possibilities. I am also sure that there are chemical possibilities related specifically to your extractant (ethyl acetone) but I have zero experience with that one. Feel free to ask me about organophosphates and oximes, which I am much more comfortable discussing...
Best Regards, Gerald