After some conversation on the Adobe forums with an Adobe supporter I finally got the point. There is a routine within the installer which adds the "-clean" parameter to the "eclipse.ini". This switch calls Eclipse to clean itself from installed modules. This is a good thing to cleanup your workspace but this should be handled very sensitive from an advanced user who knows that this parameters should be removed afterwards. But if this is added by an installer script and never removed... for sure my Eclipse always throws errors like "com.adobe... not found" if I tried to do any actions depeding on the Flex Builder. I spent so many hours on that and already quit the fight with it but now I'm very happy that I found this bug of the installer and hope this helps other people who ran into same problem.

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