Problem found.

command-not-found-data includes the amd64 parts in the i386 version of
ubuntu3, though not ubuntu2. gdbm module on i386 throws an lseek error
when you try to open those files on i386.

Remove the amd64 files and/or downgrade to ubuntu2, and your problems
will vanish.

This is obviously just a workaround though - gdbm is being dumb.

-- 
gdbm fatal: lseek error
https://bugs.launchpad.net/bugs/180368
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