Hi,
/etc/init.d/network stop and then /etc/init.d/network start brings the bond0 interface down and up as expected. Could there be an issue with when the aliases are available from /etc/modprobe.conf? There is nothing in dmesg or /var/log/messages that show the system even trying to start this interface on boot.
/sbin/chkconfig network on
Regards, Fernando.