Stolen focus

Working with AE more for the last year there are a lot of strange things about it. Performance is generally not great, even on a fast machine and it seems to be irractic when it runs well and when it does not. No other apps open, sometimes improves, other times no difference.
However, one of the more odd things is the app steals focus and will not let it go. I have to move dialog boxes to my other monitor to continue working.  Cleaning Cache often takes a very long time and both the preferences screen and the progress screen refuse to hide, remaining on top of all applications. Why? No other app does this. How is this not a bug?