There are a few possible reasons for this and the best way to ascertain the cause is to check either the \MDaemon\Logs\MDaemon-YYYY-MM-DD-AntiSpam.log file or the raw headers from the message which will typically include an X-Spam-Processed header detailing the reason.
However, the typical causes for a message not being scored include:
1. The message size exceeded the defined limit at Security -> Spam Filter -> Settings -> Don’t filter messages larger than * MB (default value on new installations is no limit):
2. The sender of the message is listed in the recipients default or white list contacts folder. As the sender exists here, MDaemon will by default assume that the sender is legitimate and not spam score an email from them. If this was the case the message would contain a header similar to the one below:
X-Spam-Processed: mail.zensoftware.co.uk, Fri, 26 May 2006 14:28:59 +0100 (not processed: sender in recipient’s private address book)
3. The message came via a trusted source defined in Security -> Security Manager -> Trusted Hosts or Trusted IPs.