Red (close) button becomes dark and windows does not close

Sometimes when I click the red (close window) button, it becomes darker and the window does not close, and the app seems inactive. I have to click the title bar (sometimes many times, the lag time to ) and the windows can close, or it can come back with the red button "normal". Very annoying when I have to close many specific windows as it completely breaks the flow of activities.
Mail seems to be a application where it happens often, but it happens also with safari, omnifocus...
Any idea how to fix this?
I use a trakpad/MBA mid 2011 OS X 10.9.4
Thanks,
Albi.

The problem is the same with Commnd-V, of course.
Here is how the button looks like,
I noticed it happens mainly when one application is active and I try to close a window which is not active.
AR

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