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Maybe this can help: Leveraging Security in the Native Platform Using Java SE 6 Technology http://java.sun.com/developer/technicalArticles/J2SE/security/
Thanks for the link, that look promising
Still seem to be having problems, I created a tiny console app to test with, at first I was getting the same 403 error as my applet but when I changed the code so that it loads the keystore using the alias that I know is on the card it worked fine. Copied the same code to the applet and it is still getting the 403 error.