Just went through a simular issue. After I changed out the valve cover gaskets on my 99 740i it began to burn smoke when I started it. Upon inspection of the intake manifold interior, it was coated in oil. After further inspection I noticed that one of the recently replaced valve cover gaskets was not seated properly and was letting air be drawn into the engine through the improperly seated gasket. We pulled the valve cover and reseated the gasket and this solved the issue.
Our theory is that the oil seperator uses negative presure on the oil seperater intake manifold valve (located at the rear of the intake manifold) to keep the intake valve closed and which keeps oil from being pulled into the intake manifold. When the gasket was not seated properly it allowed air to be drawn into the valve cover allowing the intake manifold to suck air and oil out of the engine and into the intake manifold. This is the oil that was being burnt. In addition the inside walls were getting coated with oil, when the car would sit after use this oil would drain down and pool into the air intake ports.