@Dmitrijs: did you test it as root or a normal user ? 
A normal user won't be allowed to write to /etc/apt/apt.conf.d and a message is 
printed to stderr. However it's working correctly as root but still 
disappointing for a normal user since the setting is lost upon restart.

An improved version would be to load/save from the system's setting if
run as superuser and from user's preferences if run as a normal user.

As a side note, Dmitrijs, could you please file a new report for the
crash with a backtrace if apport doesn't trigger please. Thanks in
advance.

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synaptic won't remember certain preferences
https://bugs.launchpad.net/bugs/154349
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