/usr/pluto/bin/startup-script.sh followed by a reboot of the core.
Do I understand it correctly, that you use the script and then reboot the core...or does the script cause the reboot on your core?
I am asking this, because if the script causes the reboot, then I guess your install is really fubar.
If you do a reboot after that script, then you're making a mistake, because as I understand it, the script either starts or restarts some processes (like dhcp) which didn't start or crashed during bootup.
In my experience, after I started the script, I didn't have to go to the network-settings anymore to get internet-connection on my clients...actually starting the script after reboot should be the only thing you need to do to get you going...then depending on the hardware of your md's they should be setting up and work without too much trouble.