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we are experiencing the same problem, with WebLogic 11g... Any clue how to solve it?
There is nothing strange here. Windows keeps locks on files that are open, you can't alter them as long as the file is opened by a process. So in case of Java applications running from a jar, you can't update the jar while the application is still running and by extension webstart cannot do that either.
So there is no solving to be done. Before updating an application make sure it is not running. If you don't find that a logical step, try thinking about it some more.
So you have this beautiful versioning system and you don't want to use it? This is exactly what it's for.