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 imageScreen Shot 2015-10-28 at 2.41.44 PM.png

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

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I am having the exact same problem- same version of OSX and IntelliJ. It happens on my macbook and imac.
Looking for a resolution as well.

-- Update --
There is a bug for this
IDEA-146353 3rd level pop ups hidden in OSX El Capitan Full Screen

This issue seems to be happening only when the application is in full screen mode.
When I leave full screen mode it works.

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Yes, same problem, so frustrating!

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