JNLP applets run in Plugin2 do not need codebase or absolute url in href because those can be inferred from the original html page. For example, an jnlp_href file can have only <jnlp href="applet.jnlp">.
When such applets are dragged out of browser and desktop shortcuts are created, we save documentbase and codebase in deployment cache in order to be able launch the shortcut just as run from the web.
Java Webstart has different requirement. It must have either absolute codebase or absolute uri in the href in jnlp files.
Since 6u12, desktop shortcut launch is using java webstart launcher code in order to gain relaunch capability. Because java webstart cannot parse jnlp file without knowing the codebase or absolute href, some JNLP applets cannot be launched from shortcuts.
This is a regression in 6u12 and must be fixed.