I currently have no problems with email logging. I have also got the rblsmtpd syslogd patch working its only the chkuser stuff that does not end up in syslog.
This is my configuration for qmail-smtpd. It logs everything (chkuser included).
I don't use supervise, so you must change something if you use it.
/var/qmail/ucspi/tcpserver -l my.system.name \
-b 20 -c 40 -u 88 -g 83 \
-h -R -t 5 -v -p -x /vpopmail/etc/tcp.smtp.cdb my.system.address smtp \
/var/qmail/ucspi/rblsmtpd -r bl.spamcop.net -r sbl-xbl.spamhaus.org \
/var/qmail/bin/qmail-smtpd 2>&1 | splogger mytag &
When I added a similar line where i had /var/qmail/bin/splogger tcpserver &
Please don't say similar, as similar means a lot of things: post the complete starting commands.
It appeared to actually accept all emails regardless if the user was on the system or not. When I remove that line it will reject email for invalid users using chkuser.
Probably in your configuration you have the variable CHKUSER_STARTING_VARIABLE that must be defined, or is is defined in a wrong way. Check that.