So, slow /etc/rc.d/* script delaying the /etc/rc shutdown step? Or do you have some daemon which isn't killed by its rc.d script, nor by SIGHUP, thus requiring SIGTERM and at least 10 seconds?
This is a test system and it's pretty stock right now. Aside from the standard services like pf and ntp the only installed pkg is I think dnsmasq. It's possible there's something wrong there but I'm not sure where I should start looking.