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There is a url property in TomcatManager class that isn't changed when HTTP port is changed on Tomcat Instance node. It seems that url property is defaultly set to "http://host:8080/manager" and is never changed (even when HTTP Connector port in server.xml is changed manually). The effect is that Progress dialog never stops because there is a URLWait:waitForStartup() method that relies on the TomcatManager url property.
Will try to fix for 3.6.
Fixed in trunk - the port number is not part of the URL property (same as for default instance).
Build 20040407