Now that I remember, when I was upgrading this machine to 13.04, my system partition was running out of space, and I don't know what I was thinking but I issued a "apt-get clean" in the middle of the upgrading process. This obviously aborted the upgrade and I had to finish it "manually", this may show up in the logs above. Maybe this is what caused in my case the non-executable flag of "/etc/cron.daily/apt".
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