X-[org-name]-MailScanner-SpamScore doesn't always appear

[Walt Thiessen]

We have the following key settings in MailScanner.conf:

Spam Actions = custom()
Spam Score = yes
Use SpamAssassin = %rules-dir%/spam.scanning.rules
Spam Checks = %rules-dir%/spam.scanning.rules

Most of the emails passing through the server get a value set by 
MailScanner for X-[org-name]-MailScanner-SpamScore in the message source.

However, there are a few emails where X-[org-name]-MailScanner-SpamScore 
doesn't appear at all in the message source.

Can anyone tell me why?

Walt