There is an issue with reading from the Windows certificate store with Java version 1.6.0_37, 64-bit.
This is the error log:
java.security.KeyStoreException: Windows-MY not found
It is fixed in Java 64-bit version 1.6.0_45 but unfortunately Update 45 has introduced other issues.
It is also fixed in latest 64-bit versions of Java 1.7 (1.7.0_76 for instance).