Robert,
Thanks for the quick response! Your suggestion is what makes this even more of a head-scratcher.
In the mxd, the alias for all of those fields is simply the field name itself. Using the example field I posted originally, the Alias entry is simply PropertyOwner and in the field details the Name is listed as Assessor_Info.DBO.%ParcelInfo.PropertyOwner. (See the attached screenshot)
When publishing the service, Server connect to the data with the ArcGIS Server account (which is a domain account in our case) and replaces the "DBO" with our quoted domain\user, and then fully qualifies both the field name AND the alias. For all of the fields in the parcel layer it fully qualifies the field name but the alias is simply the alias as formatted within ArcCatalog/ArcMap.
Pre-10.1, with the ODBC connection, the parcel layer field names are fully qualified and the fields from the joined table are simply the field name (not fully qualified) and the alias is simply the field name duplicated.
It almost seems like ESRI is just using the field name as the alias for joined tables when publishing rather than looking at the alias field and pushing that over, so could this be a "bug"? Doesn't solve the immediate issue but maybe there isn't an immediate solution?
If I try to use an ODBC connection, Server wants to copy the data to the server because no data source is registered (nor can be at this time). That creates a data maintenance headache due to how frequently the Assessor data gets updated and I would rather not go that route unless it is absolutely the only feasible solution.
I appreciate your thoughts on a solution to this.
BTW, this community does not thank you enough for all of the outstanding coding (and subsequent support) you have done for all of us. I, for one, could not provide my users with some of this functionality as elegantly (and especially as timely) as you have. Thanks for sharing and thank you to your employer for allowing you to spend the time!