I think you've hit upon the real falacy of typical oil "measurement". Every change to the downstream pressures and temperatures have an effect on the wellbore and reservoir flow. So with the test separator creating a different wellhead pressure than the normal flow-line/production-separator combination the well behaves differently.
In your case the new pressure results in water flow blocking oil flow for about 5 minutes while the pressures find a new equilibrium. This means to me that the volumes in the test separator are not representative of "normal" production. This is a problem if the wells have different ownership and different responses to the pressure change. If all the ownership is the same and every well responds about the same then it only matters to the reservoir engineers (who don't believe there is a problem with the data they are provided anyway) since the well production is always an allocation of physical sales based on well tests.
David