This bug also affects me.

I'm also trying to access the Firefox key store from Java and cannot do
that.

I don't see why it's so hard to load NSS by yourself. I think that the
provider should be removed from the java provider security file since it
completely breaks all Java NSS implementations that do not just want
access to the Crypto features of NSS (any FIPS or keystore operations
require NSS to be loaded differently than the nssDbMode = noDb included
in /etc/java-6-openjdk/security/nss.cfg)

Perhaps the config file located (by default) at
/etc/java-6-openjdk/security/nss.cfg could be left there and the line
"security.provider.9=sun.security.pkcs11.SunPKCS11
${java.home}/lib/security/nss.cfg" could be commented out by default.

-- 
SunPKCS11 provider auto enabled NSS problem
https://bugs.launchpad.net/bugs/580982
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