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I would strongly advise against disabling autoupdate. Oracle releases regular security updates and bug fix/enhancement releases. Disabling AU for the sake of one application puts the user at risk from malicious software. Some better alternatives:
1. Diagnose and fix the problem with the application.
2. If it is a desktop application you could bundle a dedicated JRE with it
3. If it is an applet or web start application you can of course specify a specific runtime version via JNLP. This should be a last resort as it clutters the user's machine with multiple versions of Java.