SpamAssassin not blocking GTUBE test email

Hello,

My current setup is as follows:
I-MSCP 1.4.6
Debian Jessie 8.8
SpamAssassin plugin 1.2.0

I just installed the SpamAssassin plugin according to the plugin wiki and at first it seemed to work. I saw the spamassassin score in all received emails' headers. Now the headers just show X-Spam-Checker-Version: SpamAssassin 3.4.0 (2014-02-07) on web.example.com but no score row, in spite of the email message. The same happens on regular email and GTUBE test email. I assume this is not normal behaviour? Shouldn't the GTUBE email be marked as *** SPAM ***?

Here are the logs of the time period (grepped spamd from mail.log):
http://pastat.fi/2259

The email from this row shows the score in the email header when looking at email source code:
Jun 21 13:05:39 web spamd[27657]: spamd: result: . 0 - FREEMAIL_FROM,HTML_MESSAGE,SPF_HELO_PASS,SPF_PASS scantime=4.1,size=6556,user=user1@example.com,uid=113,required_score=5.0,rhost=web.example.com.local,raddr=127.0.0.1,rport=59896,mid=<VI1PR0501MB3598DDA5B4525E88960503D8E8DA0@VI1PR0501MB3598.eurprd05.prod.outlook.com>,autolearn=ham autolearn_force=no

However, this email from another free mail provider shows no score in source, just the X-Spam-Checker-Version:
Jun 21 13:57:48 web spamd[29638]: spamd: result: . 0 - scantime=0.4,size=3753,user=user2@example.com,uid=113,required_score=5.0,rhost=web.example.com.local,raddr=127.0.0.1,rport=60014,mid=<199972887.5538108.1498042663989@mail.yahoo.com>,autolearn=ham autolearn_force=no

I am new to SpamAssassin. On server side I am more accustomed to postgrey + client side spam filtering. Now trying to move from postgrey/clientside to SpamAssassin. I am not using roundcube at all on the server. I have i-mscp configured only with RainLoop. I am using default config.php for the SpamAssassin plugin.

/var/log/mail.err looks like this:

/var/log/mail.warn looks mostly like this, I assume that the rows are just failed bruteforce attempts at the smtp auth, but now that I checked I do not seem to be able to connect with legitimate accounts either to smtp auth. This situation is probably related to the installation of the spamassassin plugin as the server has been running fine for more than 8 hours before the install:

Any help or advise is appreciated.

For the record, The SMTP auth did work after spamassassin installation, but for some reason it did meltdown as documented. Could not find anything else that would be useful in the logs.

Also, I seem to have had amavis/spamassassin/clamav installed as leftover but as far as I know I have never configured those before installing the plugin. I just installed them with the intention to configure them sometime later (this was when the server as based on ispcp, long time ago!)

Here is my master.cf

And here is main.cf

Container arch is i386.