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Note: I have only ever noticed this behavior while building platform projects, although it may extend to Java or even other types of projects as well. In this case, it may not be categorized correctly. I have always tended to build and run projects in the NetBeans IDE using the context menu of the project's node. Many of the developers I work with tend to build and run by clicking the buttons on the IDE's toolbar. There have been a number of times, dating back to at least NetBeans 5.5 (and possibly 5.0) in which running a platform project using the toolbar will yield different (and incorrect) behavior in the application after it's launched. This happened most recently this morning to a co-worker who was using NetBeans IDE 6.1 (Build 200804211638) under Java 1.6.0_06. The exact behavior varies, but today's incident prevented the TopComponent.Registry from firing any property change events to a registered listener. Another recent manifestation of the problem was that items registered into the Palette (i.e. we're using the Palette API in one of our apps) did not show up at runtime when the suite was launched via the toolbar, but did work correctly immediately thereafter when run from the context menu or from the command line in Ant. In both cases, I have verified that the suite was set as the main project. I am aware of this happening to at least five developers working on different projects. Some are in St. Louis and some are in Seattle; the people on one project have never met the others, so I rule out collusion or mass hysteria. Unfortunately, I don't (yet) have a test case or exact steps to reproduce the problem that does not involve access to source code for these applications (which I cannot disclose). If I can come up with a simple test or way of reproducing it, I will post it here.
I should have made it more clear that the workaround is to run via the context menu. This is easy to do and has worked in all cases.
Prior to 6.5, Run Main Project would "Install/Reload in Target Platform", which is inherently less reliable than just "Run", i.e. build project and start target platform. Ideally reload should work just as well, but it is dependent on various bits of code reacting correctly to changes in the system filesystem and so on. *** This issue has been marked as a duplicate of 83968 ***