I have been struggling for almost one week to get my applications up running after moving my applications from Windows 2000 to Windows 2008 R2 Server.
The procedure:
You've imported the certificate into the truststore of the JRE provided in the JDK, but you are running the java.exe of the JRE installed directly.
EDIT
For clarity, and to resolve the morass of misunderstanding in the commentary below, you need to import the certificate into the cacerts file of the JRE you are intending to use, and that will rarely if ever be the one shipping inside the JDK, because clients won't normally have a JDK. Anything in the commentary below that suggests otherwise should be ignored as not expressing my intention here.
A far better solution would be to create your own truststore, starting with a copy of the cacerts file, and specifically tell Java to use that one via the system property javax.net.ssl.trustStore.
You should make building this part of your build process, so as to keep up to date with changes I the cacerts file caused by JDK upgrades.