Crazy, the problem on this lot of hours debugging was a problem with the developer before the client!
If I start the Eclipse or Aptane App, then start the application with a popupfor asking the folder for workspace. This popup window was on my second screen, there is not in the same room. Only with Super + S was possible to see this window. I have in a bit of applications the problem, that she open windows on the wrong screen - but this is a other topic.
Now, I'm happy and so much lucky. I can work for clients with my default IDE and have a lot of fun for the next weeks, when I think about my crazy stuff on this topic.