Recent change in Datanucleus uses fully qualified name to access database objects, which is in the form of <catalog>.<schema>.<object>. However, the schema name for SQL Server has been historically set to empty string "". Therefore the fully qualified name for a SQL Server object is something like "mycatlog..mytable". With this however it cannot find an existing table in the database.
This problem demonstrates in Apache Hive bug HIVE-5218: