I ran into the problem that wake on lan is not working with freebsd and intel nic.
Shutdown the system with poweroff, WOL is not working.
if I comment out
/sbin/ifconfig -l | /usr/bin/xargs -n 1 -J % /sbin/ifconfig % down
in /etc/rc.shutdown, wake on lan is working.
the catch - after the reboot, the interface doesn't react (no IP - not even static - can be assigned). I've to poweroff the machine again (with ifconfig down) for the interface to work again.
Port LEDs stay on - with and without ifconfig down.
Here are the details:
em0: flags=8843<UP,BROADCAST,RUNNING,SIMPLEX,MULTICAST> metric 0 mtu 1500
inet 172.17.0.6 netmask 0xffffff00 broadcast 172.17.0.255
media: Ethernet autoselect (1000baseT <full-duplex>)
em0: <Intel(R) PRO/1000 Network Connection 7.3.8> port 0xbc00-0xbc1f mem 0xff6e0000 0xff6fffff irq 16 at device 0.0 on pci1
em0: Using an MSI interrupt
em0: Ethernet address: 00:15:17:31:XX:XX
Retested with FreeBSD 10.0 - Wake on Lan works.