This line (APT::Architectures "amd64 i386";) is inherited in my conf since few years ago. I was started to add i386 just in apt to query some cache. Then I updated dpkg too, but kept "garbage" in apt.conf. And this garbage was accepted by apt since this version.
dpkg conf is ok:
x@lenovo:~$ cat /var/lib/dpkg/arch
amd64
i386
x@lenovo:~$
I've just taken few minutes to clean apt.conf and finnaly removed Architecture[s] and some other unuseful settings at all.
I've seen this issue after the following upgrade (paste from history.log):
Upgrade: apt:amd64 (0.9.15.5+b1, 0.9.16.1), apt-utils:amd64 (0.9.15.5+b1, 0.9.16.1), libapt-inst1.5:amd64 (0.9.15.5+b1, 0.9.16.1), libapt-pkg4.12:amd64 (0.9.15.5+b1, 0.9.16.1)
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Daniel C