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The number of concurrent windows is set using the Number of Additional Windows a User can have Open Concurrently.
You may have designed dependencies into your filters or commands handlers that preclude them from functioning correctly when there are multiple instances open in multiple windows. In this case use the Allow this Object to be Opened in a New Window option to prevent them from being used in multiple open windows.
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The Windows menu option is not applicable to Web Browser applications.
This property is in the Identification tab.