I have not been able to find anyone else with this problem.
I upgraded to ArcGIS Server 10.1 and my table joins are not working.
I have a map service with multiple layers. I have some joins in one of those layers. I publish the map as a web service. When querying the layer (with joins) based on a map click, using the AsyncResponder, I keep getting 1000 from FeatureSet.features.length and always the first feature in the layer is added to the graphics layer. If I remove all joins and republish the service, everything works as expected (the clicked on feature is selected). What is going on here?