I recently upgraded to Ubuntu 14.04.1 LTS (trusty) and have followed the directions in https://help.ubuntu.com/14.04/serverguide/mail-filtering.html and am sending and receiving mail just fine.

While I do see X-Virus-Scanned headers in my messages, which suggests mail is indeed being processed, I do not see any X-Spam-Level or X-Spam-Score headers being added to messages. This makes downstream procmailrc and client-side filtering ...more difficult.

While having $final_spam_destiny = D_DISCARD in /etc/amavis/conf.d/20-debian_defaults does greatly reduce spam to my inbox, I had concerns of false-positives prior to tuning and didn't know were there going, so have set it to D_PASS for the time being. This exposed the problem.

I'm not sure where to look to start diagnosing the problem (otherwise I'd post a suspect configuration file).

/etc/amavis/conf.d/15-content_filter_mode has the lines uncommented to enable virus and spam checks, and virus checking appears to be working according to the headers.

Spam Assassin certainly seems to be starting just fine, too.

SpamAssassin debug facilities: info
SA info: zoom: able to use 360/360 'body_0' compiled rules (100%)
SpamAssassin loaded plugins: AskDNS, AutoLearnThreshold, Bayes, BodyEval, Check, DKIM, DNSEval, FreeMail, HTMLEval, HTTPSMismatch, Hashcash, HeaderEval, ImageInfo, MIMEEval, MIMEHeader, Pyzor, Razor2, RelayEval, ReplaceTags, Rule2XSBody, SPF, SpamCop, URIDNSBL, URIDetail, URIEval, VBounce, WLBLEval, WhiteListSubject
SpamControl: init_pre_fork on SpamAssassin done

I've also set $log_level = 2; in /etc/amavis/conf.d/50-user and don't see any obvious errors rolling by in the logs.

Q: Any recommendations of what to try next?

UPDATE (it appears that I have the right setting already):

/etc/amavis/conf.d$ grep sa_tag_level_deflt *
20-debian_defaults:# $sa_tag_level_deflt  = 2.0;  # add spam info headers if at, or above that level
20-debian_defaults:$sa_tag_level_deflt  = -999;  # add spam info headers if at, or above that level