Ok It would appear having java running while performing the update is what buggered it up, we are all happy now.
I got a lot of help from the java-dev mailing list. Turns out rerunning the SecUpd2005-002 security update did the job, someone on the list also suggested running "sudo update_prebinding", which will sort the java issues as well, I can't confirm this as I think I ran the update,erm I was a wee bit pissed - something I can not recommend.

Oh a different note just got back from the Swans v Crows - go the crows. Was a good game if not very long for those of us who were hungover :(