Modal dialogs are hidden behind in El Capitan

Am on Mac OS X El Capitan - Just updated yesterday.
Since then whats happening is that a modal dialog that should appear in front is totally hidden, And this being a modal dialog there is no way to get out if this either. So many time you just cannot click the button and so will have to force quit. This did n't seem to be the case before.

Refer above image

Any suggestions ? This is mostly making IntelliJ unusabe. The version I run is 14.1.5