JBossAS 5 will be the first version supported on JDK 5. All of the 4.2.x versions are supported only on JDK 5, and the 4.0.x versions are supported on JDK 5 and 1.4.2.
So even if you could get JBossAS 4.0.3.sp1 running on JDK 6, it would not be supported.
If you really need JDK 5 support, Sun will provide it: http://www.sun.com/software/javaseforbusiness/index.jsp. The only thing their warning on the JDK 5 download page means is to not expect more free updates. If you want updates, you will have to pay for them.
Thanks for your help