How do I sign a Java applet for use in a browser?
3 easy steps
keytool -genkey -keystore myKeyStore -alias me
keytool -selfcert -keystore myKeyStore -alias me
jarsigner -keystore myKeyStore jarfile.jar me
Perhaps it's because you're opening some .class files outside the jar file?
That way it may not display the warning. I tried doing it that way but it still showed me the certificate warning and for a simple case it actually prevented me from accessing a class from the JAR with the separated class.
Maybe your specific setup or file organization causes that behavior. If you can layout that in more detail we could help better (or rather, try putting all those .class files in yet another signed Jar and add it to the archive"..., anotherJar.jar").
First, I'd suggest getting a valid code signing certificate. You can get a free cert from Thawte. Although generally these certs are used for S/MIME, they are also valid for code signing.
The second option is to import your self signed cert into the cacert file of the JRE which your browser is invoking.
The next thing to check is to make sure your browser is running your latest jar. One way to do this is to always increment your version number. The other option is for you to clear your Java applet cache. I usually clear my browser's cache as well, but this shouldn't be needed.