FortiGate Next Generation Firewall utilizes purpose-built security processors and threat intelligence security services from FortiGuard labs to deliver top-rated protection and high performance, including encrypted traffic.
This article describes a root cause for the following symptom : The FortiGate does not log some events on the syslog servers.
FortiOS 4.0 MR3
FortiOS 5.0

A possible root cause is that the logging options for the syslog server may not be all enabled.
This must be configured from the Fortigate CLI, with the following command :

FGT# config log syslogd filter
FGT (filter) # get                             <== to display your current config, which looks like this in FortiOS 4.0MR2 :
app-ctrl            : enable
attack              : enable
dlp                 : enable
email               : enable
forward-traffic     : enable
invalid-packet      : enable
local-traffic       : enable
netscan             : enable
severity            : information
traffic             : enable
virus               : enable
voip                : enable
web                 : enable
analytics           : enable
anomaly             : enable
app-ctrl-all        : enable
blocked             : enable
discovery           : enable
dlp-all             : enable
dlp-docsource       : enable
email-log-google    : enable
email-log-imap      : enable
email-log-msn       : enable
email-log-pop3      : enable
email-log-smtp      : enable
email-log-yahoo     : enable
ftgd-wf-block       : enable
ftgd-wf-errors      : enable
infected            : enable
multicast-traffic   : enable
oversized           : enable
scanerror           : enable
signature           : enable
suspicious          : enable
switching-protocols : enable
url-filter          : disable
vulnerability       : enable
web-content         : enable
web-filter-activex  : enable
web-filter-applet   : enable
web-filter-command-block: enable
web-filter-cookie   : enable
web-filter-ftgd-quota: enable
web-filter-ftgd-quota-counting: enable
web-filter-ftgd-quota-expired: enable
web-filter-script-other: enable

You can then use the command set <option> enable/disable to enable or disable any of the items in the list.
Example :

FGT (filter) # set url-filter enable
FGT (filter) # end

A logging test can be made with the following CLI command : "diagnose log test"

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How to perform a syslog and log test on a FortiGate with the 'diagnose log test' command