after going nuts thinking that I had infact lost my marbles and had been following the instructions wrong I have discovered (thanks to Mr Andrew Frayling) that there is something missing from the Jira server.xml file.
A config changed happened between Tomcat 5.5 and 6 ( JIRA 4.0 uses 5.5, JIRA 4.1 uses 6 ) which means that you must have SSLEnabled=”true” in the secure connector port of the JIRA config – this is missing. Add it in and SSL suddenly starts working !!
It was drving me nuts all weekend!!
and now it works .. HURRAH 😉