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When running an application server (JBoss3) using the AppServer controls, it appears to always run in Debug mode even when the launch mode is set to Run for that server.
The difference between run and debug modes is whether or not breakpoints will be honored. Are you seeing breakpoints honored when launching in Run mode?
Thanks for this report. Execution should not be halting at breakpoints when in Run mode. I have entered an issue into our tracking system on this topic.