Tony Godshall wrote:
Uh, your dlocate seems to show no /etc/apt/apt.conf file either.
Nor here: http://packages.debian.org/cgi-bin/search_contents.pl?searchmode=filelist&word=apt&version=stable&arch=i386&page=1&number=all There seem to be a number of contexts in which conffiles aren't regarded as "first class citizens," much to my annoyance.
I do have a directory /etc/apt/apt.conf.d I'll shut up now and let this thread return to the original question.
Don't worry, the original question seems to have been resolved (or was apparently a false alarm).