How is the configuration of an ester enolate double bond assigned according to CIP?
Whilst the (E)/(Z) nomenclature works fine for enolates of ketones and aldehydes, there is, as you've discovered an issue with the assignment of enolate geometry for esters (an amides and thioesters) since depending on the nature of the ester and the metal counter-ion used, we end up with a different answer. 

Whilst the CIP rules are trivial to apply to any enolate, their use is not always conducive to describing the chemistry going on, especially when we end up with (E) and (Z) enolates both giving syn-adducts (for example) merely because we've changed a counter-ion (the actual spacial configuration of the enolate is identical in both cases).  



To avoid this switching of configurations, we usually choose some other way of definition such that at the beginning of any thesis or SI where enolates are used, there is usually a statement that explains the way in which the author is planning to define their enolates (i.e. define them however you wish, but make sure you define them). 

This is often not in agreement with formal CIP rules for the reasons outlined above, or at least not consistently in agreement with CIP rules (things may happen to end up named correctly regardless of how we define them). 

This statement defining the enolate geometry is generally a re-hash of Prof Evans who stated: 


  ...irrespective of the formal CIP criteria, the O-atom bearing the metal (the OM residue) is given a higher priority, and the ipso-substituent X (in enolates) the lower one...


Whilst this is widely accepted, there are some issues, mainly because there are inconsistencies between groups: Evans' calls it (E) but Myers' calls it (Z) with Furstner calling it (E) but for a totally different reason than Evans'.  For this reason alone, its always worth looking at the actual schemes and defining the enolate yourself rather than trusting that enolate X gives Y.

This issue is the source of the major objection to Evans' idea about the nomenclature. The whole reason we use E/Z/R/S is because they are well defined, I can tell you that I have (R)-..... and you'll know what I'm talking about, because we both follow the same rules, and if you don't, you're wrong. 

The proposed solution to Evans' solution (Ernest Eliel) is to stop messing with these well defined descriptors, and instead go back to using cis and trans for enolate geometry, as these terms are less well defined and as such abusing them in this way doesn't lead to any significant confusion.