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emacs holding focus, not granting it to xterm


I'm running cygwin x on my laptop [version 1.7.29(0.272/5/3), Windows 7 prof], start windows on
remote machines (cygwin and linux mint), that are exported to my laptop. I've noted the problem for
more than a year now and it's irritating still, new versions of cygwin and applications notwithstanding.

Here's what happens:
I enter text into emacs, move mouse to an xterm, click and enter text there, but text is going into
emacs. I can only move keyboard flow away from emacs after having done some nuisance operations in
the emacs window, like moving around the pointer; it mostly helps with one such instance, sometimes
I have to repeat. It's rather unpredictable. The raised status of the xterm window, however, is
deceiving me. So text goes even into hidden emacs windows.

Vague guess: Something's waiting in emacs to get satisfied so it would release the keyboard
association.

I don't want focus-follows-mouse without a click for focus shift. So I haven't tried this option.
Would expect it wouldn't help. Is there an environment setting that would help? Anything else to get
rid of the glue?

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