I am experiencing this problem with both Firefox and Thunderbird (and
have lost many e-mail messages because my typing suddenly went to the
index window and was interpreted there as a "delete").

Contrary to the original poster, I have the problem only with keyboard
events, never with mouse events. Klicking, dragging, marking all works
fine on the foreground window. Key strokes suddenly start going to the
background window. Switching the foreground between windows does not
help. Closing and restarting the whole application usually helps.

My workaround in Thunderbird is to create an empty folder and switch the
index window to it before typing a message, so the stray keystrokes
cannot do much damage. In Firefox I use tabs instead of windows.

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https://bugs.launchpad.net/bugs/1231588

Title:
  Running unclutter without "-noevent" causes focus problems for Firefox
  and Thunderbird

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