I'm assuming youre not using any custom template to rewrite the message before its outputted. In which case it will use the time provided by the sending host. If the sending host doesnt provide a microsecond value in the timestamp, microseconds will always be 0s. If you want higher granularity, you either need to configure the sending host to do so, or create a template with the R_ISODATE value (uses received time instead of sent time).

Sent: Monday, July 12, 2010 11:01:22 AM
From: Daniel Maher <dma+syslogng@witbe.net>
To: syslog-ng@lists.balabit.hu
Subject: [syslog-ng] ts_format(iso); frac_digits(6); == 000000+00:00 always ?

Hello,

I wish to enable the ISO timestamp format, and to have a granularity of 
six digits.  I have enabled the following in my global options :

   frac_digits (6);
   ts_format(iso);

The timestamp format is enabled as expected, but the fractional digits 
always appear as straight zeros.  For example :

2010-07-12T16:49:27.000000+00:00 s_sys@srv-01 postfix/qmgr[2851]: 
2EF1B1F9034E: removed

Is there a way to enable the desired millisecond timestamps ?

Details :

$ uname -s -r -v -p -o
Linux 2.6.18-194.el5 #1 SMP Fri Apr 2 14:58:14 EDT 2010 x86_64 GNU/Linux
$ cat /etc/redhat-release
CentOS release 5.5 (Final)
$ rpm -qa | grep syslog-ng
syslog-ng-2.1.4-1.el5

Thank you, and have an excellent day.