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Michael,
A published map with annotation works fine in a map service when you add the map service as a dynamic layer. You can see this in may flex site including my own.
http://gis.calhouncounty.org/flexviewer2.0/
Sean,
Both dynamic labeling and Actual Annotation Feature classes will display in the Map as Long are the layer is specified as other than feature.
I just gave that a try. The anno layer is only turned on, with all of the other layers off. However, I still have missing symbology and labels. I still have to turn on my parcels under the grouped anno layer to see my parcel pins, for example. I would like it so that in the table of contents, checking a box next to a feature turns off the symbology, as well as the label. Can you provide me with any example? I am pretty new to flex. Thanks for the quick response.