Hmm, after the workaround was suddenly turned off, I reapplied it, and found 
that /etc/apt/preferences.d had corrupted. Instead of a directory it turned 
into a file which crashed apt-get. Opening the file showed nothing of interest 
(an empty file) while it was about 13KB in size.
I had the same problem a few weeks ago (or maybe some months) but instead of 
preferences.d it was apt.conf.d that turned into a file, and sources.list got 
corrupted. I remember opening sources.list, and at the end of the file it just 
stopped without closing. This has been a while ago, but it could well have been 
at the same time the workaround wasn't active since I did remove the workaround 
in that time.

Also, #19 indicates that it appears every hour, which could prove that
it's apt checking for updates. I'm just speculating though, it could be
coincidence. I don't know how many times an hour apt checks for updates,
but if it's an hourly schedule, it's worth checking which command
triggers the bug. I suppose apt itself is not the problem as it probably
just calls some command in a library, right?

I hope to be of assistance this way...

-- 
udisks-probe-ata-smart causes HSM violations
https://bugs.launchpad.net/bugs/574462
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