(I am an occasional spambayes developer)

This behaviour is by design. future versions are likely to offer other
storage options which do not have this problem (possibly based on zodb).

Short-term solutions include:

a. Configure procmail to use a lock file, and use a wrapper script
around sb_filter.py for training which also uses the 'lockfile' utility
to serialise access to your database.

b. Replace all uses of sb_filter.py with sb_bnfilter.py. This behaves
(almost) identically, but all operations are automatically dispatched
through a shared, automatically managed daemon process. The primary
purpose of this is to reduce startup overhead, but it will also
eliminate the concurrency which causes this corruption.

I hope this helps,

-- 
sb_filter.py does not lock the database file resulting in corruption
https://launchpad.net/bugs/30720

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