Thank you Dominik. I thought I had tested /etc/apt/preferences but
obviously I had not.

Under Karmic aptitude does respect the policies set in
/etc/apt/preferences but not preferences.d/*. The tools apt-cache and
apt-get also respect the policies in /etc/apt/preferences.

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Aptitude ignores apt_preferences
https://bugs.launchpad.net/bugs/508545
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