Comment 6 for bug 852181

Added precise tag since it still had the wrong indication that applications are updated.
After upgrading over 130 packages today the issue seems to be solved.
The upgrade also incl. aptdaemon which obviously solved other bugs too (attached history.log).
After update and reboot, open update-manager via dash, reload package cache, update-manager presents updates and indicator-session displays updates available.
I'll monitor the next days if it's randomly solved or fixed for good.