My program works fine from winNT and on the AS/400 using the Toolbox driver( com.ibm.as400.access.AS400JDBCDriver). However, it doesn't work using the native driver (com.ibm.db2.jdbc.app.DB2Driver). What did I miss?

I can't be sure from the information given, but the most likely cause is that not only the driver class but also the JDBC database URL is different for the two drivers. For the Toolbox driver, use:

jdbc:as400://MACHINENAME/COLLECTIONNAME

For the native driver, use:

jdbc:db2:localhost/COLLECTIONNAME