If I publish a map with table to table joins or relates, the tables loose there joins and/or relates when published. A simple example is get 2 tables on a blank map (you will have to add a feature class also to publish), do a table to table join or relate and publish it as a map service with only mapping capabilities and default settings. SDE is in data store and no data gets copied.
A feature class to table join or relate publishes just fine. My tables sit in a SDE and the fields being joined are indexed.
I didn't have this problem in 10.0 and when upgrading it broke parts of my code. I know I can do a view but this seems to be a bug or breaking change in 10.1 SP1. I skipped over the 10.1 release so I don't know if it happened there.
Edit: Another thing I just found out. If you join or relate a table to a feature class, that also does not work.
I accomplished this by creating a new View in ArcCatalog, which is similar to a Query Layer. The issue is I can't publish a view in a feature service. I haven't tried publishing a query layer in a feature service, but I assume it also won't publish. So because table to table joins do not work, I am forced to publish a new map serivce to accomplish this goal.