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AHH Update, I got a response from the devs and they said this whole thing was actually just a feature not a bug. If you navigate to Window > Preferences > General > Startup and Shutdown > Plugins activated on startup
you see a list of all the plugins that startup with Eclipse, we allow people to shut down portions of MyEclipse that they don’t use. In the case of “Fakeworkspace” you have a lot (almost all of the connectors) turned off, including weblogic and websphere, so what was happening is those connectors weren’t starting until you forced them to by opening their preferences.
