When the run console is floating and I start a run configuration (without showing run config settings dialog) the Idea main window and the floating run window steal each other the focus which results in a never-ending flickering. That seems to be related to the Messages tool window: Steps to reproduce:

• Run window is floating
• Check javac option "Report use of deprecated features" is enabled
• When starting a run configuration that uses a deprecated field/method, the messages window comes up and stays open. Then, the two tool windows "Messages" and "Run" endlessly steal the focus of each other.

There are two workarounds I figured out: 1. minimize the Idea main window, wait two to five seconds and restore it. Then the focus can be set to the run window manually after clicking in one of the tool windows - but that's quite awkward. 2. if deprecated features are not reported at all, the problem doesn't occur - but that's obviously not a better solution (however I could live with this alternative much better than with the first one). When removing the use of the deprecated field/method, the messages window shortly comes up during make and is hidden again and no flickering occurs. I also deleted the IWS file (which seemed to help for the same bug in Idea 4.5/5.0) but that doesn't help for Demetra (Build 5181). The bug is always reproducible with different projects. If the messages window is fixed in the Idea main window the flickering appears between the Idea main window and the run window.