Ok, I realized that for some reason, any applications were gaining
focus.

I fixed following this answer into askubuntu:
http://askubuntu.com/questions/128738/when-i-launch-an-app-the-focus-
doesnt-move-to-the-opened-app

Run in a terminal:

gconftool-2  --type=Integer --set
/apps/compiz-1/general/screen0/options/focus_prevention_level 0

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https://bugs.launchpad.net/bugs/627195

Title:
  Window management - Apps raised from indicators sometimes dont have
  the focus

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