This may occur if:

• there are triggers defined on the tables
  If you have a trigger defined on a table that inserts data into another table on INSERT, DELETE, or UPDATE, the data in the tables will change as the upgrade is run, which will cause unpredictable results.
  To avoid this, select the Disable DML triggers data packaging option before you generate the package.
• primary keys are defined on columns with differing collation order
  If you upgrade tables that have primary keys defined on columns that have different collation order, SQL Packager may produce unpredictable results.
• columns contain timestamp data
  SQL Packager can not upgrade data in timestamp columns.
• tables do not have identical schema
  If the structure of the tables you are upgrading is not identical, SQL Packager may produce unpredictable results.

If you continue to experience problems, please contact Red Gate Support.