Is it possible to access certificates stored in the Local Machine store (rather than Current User) from a Java Servlet? I've tried using the MSCAPI provider opening the "Windows-MY" and "Windows-ROOT" stores, but neither contain certificates from the Local Machine store.
The default JDK implementation is fairly limited. AFAIK it will only bring back RSA keys and certificates. It is not a general purpose adapter to MSCAPI. I have been able to get some certs back using the mechanism you describe.