Something I have noticed is that identify and query through the Flex viewers and REST services do not report any values described with domains from a geodatabase.
If you add a service in ArcMap and/or ArcGIS Explorer, and identify a feature, you will get the description and not the code. But if you use a Flex viewer and/or the REST Services Directory, the code will be reported, not the description from a domain in the geodatabase.
I really need some help figuring this out right now.