The original bug report said that you were running:

Version: 0.93.1-1
ii  libdb4.2                    4.2.52-17    Berkeley v4.2 Database Libraries

and your problem occurs with both:
bogofilter_0.93.3.1-1_i386.deb
bogofilter_0.93.5-1_i386.deb

You say that bogofilter_0.93.1-1_i386.deb works and then go on to say:

"At least bogofilter_0.93.1-1_i386.deb or the one before works without 
crashing the db file."

This is because your log format needs to be updated to the new format,
as the NEWS.Debian file indicates. Version 0.93.1 depended on libdb
4.2.25 (as you correctly have in the original report), moving to
0.93.0-2 or anything newer requires you to upgrade your libdb to 4.3
and perform the NEWS.Debian log format change procedure. 

I had this same problem because I didn't think I needed to perform the
log format upgrade, but I was wrong. As soon as I did it, things
worked fine again.

I suggest that you either go through the more painful proceedure of
dumping your wordlists to .txt files, destroying your DB environments
and then recreating them by reloading your wordlist.txt files, or
follow the steps outlined in the NEWS.Debian to upgrade your wordlist
databases. 

I am fairly confident that you will then find that your problem no
longer exists, as this is exactly what I had to do to make the problem
go away.

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