Comment 24 for bug 574462

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...