Problem: Joins that use ODBC connections on Windows are not supported by the ArcMap server on Unix
When using an ODBC connection to connect to a database such as MySQL in ArcGIS Desktop on Windows, the connection is not retained when the map document is moved to Unix and published on ArcGIS Server.
This is a known limit.
Solution or Workaround
Joins with DBF tables and ArcSDE tables are retained, when moving the map document to Unix.
If the size of the data permits, the table could be stored as a DBF file, which is periodically updated (by an operating system scheduled task, for example). In such a case, a non-pooled ArcGIS Server service should be used to get the map data updated upon each session.
Table data could be managed by a database system that is supported by ArcSDE. If an open source database system is required, PostgreSQL can serve as the open source database system. See the link to the System Requirements matrix for ArcSDE in the Related Information section for more information.