Heres something that could be related?
Setting up ca-certificates-java (20110912ubuntu3) ...
Installing new version of config file /etc/ca-certificates/update.d/jks-keystore
 ...
        at sun.security.x509.AlgorithmId.<init>(AlgorithmId.java:114)
        at sun.security.x509.AlgorithmId.parse(AlgorithmId.java:381)
        at sun.security.x509.X509Key.parse(X509Key.java:168)
        at sun.security.x509.CertificateX509Key.<init>(CertificateX509Key.java:7
5)
        at sun.security.x509.X509CertInfo.parse(X509CertInfo.java:705)
        at sun.security.x509.X509CertInfo.<init>(X509CertInfo.java:169)
        at sun.security.x509.X509CertImpl.parse(X509CertImpl.java:1747)
        at sun.security.x509.X509CertImpl.<init>(X509CertImpl.java:196)
        at sun.security.provider.X509Factory.engineGenerateCertificate(X509Facto
ry.java:107)
        at java.security.cert.CertificateFactory.generateCertificate(Certificate
Factory.java:322)
        at sun.security.provider.JavaKeyStore.engineLoad(JavaKeyStore.java:763)
        at sun.security.provider.JavaKeyStore$JKS.engineLoad(JavaKeyStore.java:5
5)
        at java.security.KeyStore.load(KeyStore.java:1201)
        at UpdateCertificates.createKeyStore(UpdateCertificates.java:65)
        at UpdateCertificates.main(UpdateCertificates.java:51)
Caused by: java.io.FileNotFoundException: /usr/lib/libnss3.so
        at sun.security.pkcs11.Secmod.initialize(Secmod.java:186)
        at sun.security.pkcs11.SunPKCS11.<init>(SunPKCS11.java:197)
        ... 31 more
done.


... and 

Setting up ca-certificates-java (20110912ubuntu3) ...
Installing new version of config file /etc/ca-certificates/update.d/jks-keystore ...
Exception in thread "main" java.security.ProviderException: Could not initialize NSS
        at sun.security.pkcs11.SunPKCS11.<init>(SunPKCS11.java:201)
        at sun.security.pkcs11.SunPKCS11.<init>(SunPKCS11.java:103)
        at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
        at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstruct

 installed by openjdk-6
onstructorAccessorImpl.java:45)
        at java.lang.reflect.Constructor.newInstance(Constructor.java:532)
        at sun.security.jca.ProviderConfig$3.run(ProviderConfig.java:262)
        at sun.security.jca.ProviderConfig$3.run(ProviderConfig.java:244)
        at java.security.AccessController.doPrivileged(Native Method)
        at sun.security.jca.ProviderConfig.doLoadProvider(ProviderConfig.java:244)
        at sun.security.jca.ProviderConfig.getProvider(ProviderConfig.java:224)
        at sun.security.jca.ProviderList.getProvider(ProviderList.java:232)
        at sun.security.jca.ProviderList.getService(ProviderList.java:330)
        at sun.security.jca.GetInstance.getInstance(GetInstance.java:157)
        at java.security.Security.getImpl(Security.java:696)
        at java.security.AlgorithmParameters.getInstance(AlgorithmParameters.java:130)
        at sun.security.x509.AlgorithmId.decodeParams(AlgorithmId.java:121)
        at sun.security.x509.AlgorithmId.<init>(AlgorithmId.java:114)
        at sun.security.x509.AlgorithmId.parse(AlgorithmId.java:381)
        at sun.security.x509.X509Key.parse(X509Key.java:168)
        at sun.security.x509.CertificateX509Key.<init>(CertificateX509Key.java:75)
        at sun.security.x509.X509CertInfo.parse(X509CertInfo.java:705)
        at sun.security.x509.X509CertInfo.<init>(X509CertInfo.java:169)
        at sun.security.x509.X509CertImpl.parse(X509CertImpl.java:1747)
        at sun.security.x509.X509CertImpl.<init>(X509CertImpl.java:196)
        at sun.security.provider.X509Factory.engineGenerateCertificate(X509Factory.java:107)
        at java.security.cert.CertificateFactory.generateCertificate(CertificateFactory.java:322)
        at sun.security.provider.JavaKeyStore.engineLoad(JavaKeyStore.java:763)
4)
        at sun.security.provider.JavaKeyStore$JKS.engineLoad(JavaKeyStore.java:5
        at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
        at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57)
        at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
        at java.lang.reflect.Constructor.newInstance(Constructor.java:532)
        at sun.security.jca.ProviderConfig$3.run(ProviderConfig.java:262)
        at sun.security.jca.ProviderConfig$3.run(ProviderConfig.java:244)
        at java.security.AccessController.doPrivileged(Native Method)
        at sun.security.jca.ProviderConfig.doLoadProvider(ProviderConfig.java:244)
        at sun.security.x509.X509CertInfo.parse(X509CertInfo.java:705)
        at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
        at sun.security.x509.X509CertInfo.parse(X509CertInfo.java:705)
        at sun.security.x509.X509CertInfo.<init>(X509CertInfo.java:169)
        at sun.security.x509.X509CertImpl.parse(X509CertImpl.java:1747)
        at sun.security.x509.X509CertImpl.<init>(X509CertImpl.java:196)
        at sun.security.provider.X509Factory.engineGenerateCertificate(X509Factory.java:107)
        at java.security.cert.CertificateFactory.generateCertificate(Certificate
        at java.security.cert.CertificateFactory.generateCertificate(CertificateFactory.java:322)
        at sun.security.provider.JavaKeyStore.engineLoad(JavaKeyStore.java:763)
        at sun.security.provider.JavaKeyStore$JKS.engineLoad(JavaKeyStore.java:55)
        at java.security.KeyStore.load(KeyStore.java:1201)
        at UpdateCertificates.createKeyStore(UpdateCertificates.java:65)
        at UpdateCertificates.main(UpdateCertificates.java:51)
        at sun.security.jca.ProviderConfig$3.run(ProviderConfig.java:262)
        at sun.security.jca.ProviderConfig$3.run(ProviderConfig.java:244)
        at java.security.AccessController.doPrivileged(Native Method)
        at sun.security.jca.ProviderConfig.doLoadProvider(ProviderConfig.java:244)
        at sun.security.jca.ProviderConfig.getProvider(ProviderConfig.java:224)
        at sun.security.jca.ProviderList.getProvider(ProviderList.java:232)
        at sun.security.jca.ProviderList.getService(ProviderList.java:330)
        at sun.security.provider.X509Factory.engineGenerateCertificate(X509Facto
        at sun.security.provider.X509Factory.engineGenerateCertificate(X509Factory.java:107)
        at java.security.cert.CertificateFactory.generateCertificate(CertificateFactory.java:322)
4)
        at sun.security.provider.JavaKeyStore.engineLoad(JavaKeyStore.java:763)
        at sun.security.provider.JavaKeyStore$JKS.engineLoad(JavaKeyStore.java:5
        at sun.security.provider.JavaKeyStore$JKS.engineLoad(JavaKeyStore.java:55)
        at java.security.KeyStore.load(KeyStore.java:1201)
        at UpdateCertificates.createKeyStore(UpdateCertificates.java:65)
        at UpdateCertificates.main(UpdateCertificates.java:51)
Caused by: java.io.FileNotFoundException: /usr/lib/libnss3.so
        at sun.security.pkcs11.Secmod.initialize(Secmod.java:186)
        at sun.security.pkcs11.SunPKCS11.<init>(SunPKCS11.java:197)
        ... 31 more
done.