To confirm the performance loss, I would execute the same query using the same driver using JUnit or from a simple Java main method. Unlikely to be a JBoss problem per se. PL/SQL will be faster, but no an order of magnitude faster.
What is the total query time in the 2 examples given?
You will have an overhead from java compared to
plsql before the actual query is processed on the DB and after the query is finished and the result is transfered back to your application. For very small queries you could end up with this result. If the query is more heavy you shouldn't notice the difference.