Yes, Windows Server 2003 support IPv6.
Are you running JDK 5? I do not think that 1.4.2 support IPv6.
I do not think that JBoss AS 4.0.x supports IPv6. Even in 4.2.x and 5.0.0 there are issues. See for example https://jira.jboss.org/jira/browse/JBAS-6390 which notes a problem that is not fixed until 4.2.4 or 5.0.1.
You might also want to search JIRA with "IPv6" to find out all of the issues.