This bug seems to be a bad interaction between lightdm and fglrx.
I switched to GDM and now the problem does not happen anymore.

** Also affects: lightdm
   Importance: Undecided
       Status: New

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which is subscribed to fglrx-installer in Ubuntu.
https://bugs.launchpad.net/bugs/1067320

Title:
  1002:6798 [fglrx] VT cursor is visible and blinking on top of Unity
  Radeon HD 7970 and 5450

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