My guess is that it's related to having multiple *.Contents-ARCH.gz
files around.

Please post the output of
apt-file -v search foobar | grep "^D: Search in"

The "-v" should display debugging info, which I'm interested in.

On my hardy system it looks like:
D: Search in 
\/var\/cache\/apt\/apt\-file\/archive\.ubuntu\.com_ubuntu_dists_hardy_Contents\-i386\.gz
D: Search in 
\/var\/cache\/apt\/apt\-file\/de\.packages\.medibuntu\.org_dists_gutsy_Contents\-i386\.gz

** Changed in: apt-file (Ubuntu)
   Importance: Undecided => Medium
     Assignee: (unassigned) => Daniel Hahler (blueyed)
       Status: New => Incomplete

-- 
apt-file search prints all results twice
https://bugs.launchpad.net/bugs/174134
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