Comment # 6 on bug 952799 from Matthias Andree

Be sure to check 
* for configuration files in use, because those can tell bogofilter what
database files to look for (and those won't differ between executable versions)
* for what the alternatives package has actually set.  bogofilter-db reporting
as bogofilter-kyotocabinet looks fishy.  You may want to trace with "which" and
with looking at symlinks and tracing them, possibly with readlink or ls -l
WITHOUT -H or -L options.