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I have a web application that downloads a jar file from the web server using java web start. The jar is signed using J2SE security tool. However, I get the security warning "The application digital signature cannot be verified. Do you want to run the application?" Am I missing something that is causing this??

+1  A: 

If it is self-signed you also need to add the certificate into windows certificate store.
If you use a Certificate Authority such as Verisign then you will not have the problem.

See here for an explanation (from Verisign) on why to sign from them.

Romain Hippeau