Comment # 8 on bug 952799 from Matthias Andree

@Maciej, I posted relevant commands to print the configuration in use, and the
default configuration, to the bogofilter list where this was also reported.  If
there is a configuration file in place, it may overwrite the location and/or
name of the bogofilter data file!

bogofilter -QQ

bogofilter -QQ -C

And also the manual page has a files section.

We really need to establish a. what the packaging should be (I haven't found
anything obviously wrong in the .spec file) and b. what your system actually
provides.  

You also really need to trace the symlinks from the surmised executable through
the update-alternatives maintained symlinks (with ls -l or namei or readlink or
so).

Without such information, that's hard to debug.