Don't think ESRi will solve the problem. Too few complaints, the Explorer is delivered "as is" and ... it's free.
The workaround I use : Defining the unique values in ArcGIS Webmap, saving the map with the new layer off, opening the map in Explorer, switching the new layer on and then finalizing the layer's update (fields, popups, ...).
It raises the risk of errors during the sites switching and is whatever a waste of time but if you can't wait ESRI's good will, it will do the job.
Have fun !