When you switched from Persistence.createEntityManagerFactory to @PersistenceContext, you switched from Java SE style setup to Java EE. In the latter option you use <jta-data-source> element to specify the datasource, or the GlassFish server provides you with one (Derby/JavaDB that comes with it), but the jdbc properties are ignored.
If you want to use Derby, start it <gf>/bin/asadmin start-database, otherwise create the connection pool and resource, and specify the resource name in the <jta-data-source> element of your persistence.xml.
thanks,
-marina
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