Matt,

> Unfortunately the problem system is the one currently in production so I
> will experiment elsewhere. I have downgraded the spamassassin on my
> "standalone" system and it is still producing dramatically different
> results. I will try installing same version of amavis on that system
> with no chroot and see if the same thing occurs.

The version of amavisd-new should not have any effect on SpamAssassin scores.

Use the same version of SpamAssassin and the same set of rules
(like SARE rules, same sa-update channels, local.cf, *.pre,
bayes db, awl, ...).

> It seems very odd that 
> when amavis is not involved the scores always come out to the nearest
> 0.1, but with amavis I have scores like 5.876.

Make sure to always run a command-line spamassassin under the same
user as amavisd daemon is running with (vscan).

See also:
  http://www.ijs.si/software/amavisd/#faq-spam

and search for "SpamAssassin returns different score ..."

  Mark

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