terminator: reproducable
gnome-terminal: reproducable
xterm: not reproducable
konsole: not reproducable

I also noticed that the location of the mouse pointer matters when you
switch from terminator/gnome-terminal to gedit: the mouse pointer should
not be over the terminal window. If the mouse pointer is eg over a
panel, the effect will occur, if the mouse pointer was over the terminal
and you alt-tab into the gedit windows, it won't work.

-- 
gnome terminal doesn't leave "select" mode and keeps overwriting clipboard and 
makes selecting in gtk applications impossible
https://bugs.launchpad.net/bugs/502499
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