ENDIAN Firewall - SMTP Spam Filter

I've upgraded my endian community firewall software from version 2.2 to 2.3 and restored the backup settings to configure the new version. However it appears that everything is not working as it should. For some reason when Mail Spam Filter is enabled in Proxy>SMTP only some of my e-mail are let in, others appear to arrive and are scanned by endian but are not forwarded to mailboxes. If the spam filter is disabled all e-mails come in correctly however this includes a great deal of spam. Am I missing a trick? Is there another setting I need to have in place? Why are some e-mails allowed in but others blocked? The 2.2 version was working fine until ClamAV decided to reach it's end of life and therefore forced me to upgrade Endian. Grateful for any help I can get!