I found today that it's possible to re-order the interfaces in endian through the console. This is a big help and allowed me to properly configure my machine in a way I didn't think was possible.
In regards to my original post, the user who posted after me, the issue was that the Setup which says will be run is not run. I'm sure this is actually in reference to WebGUI setup wizard which is presented to the user when logging in for the first time through a web browser. The wording on this dialog should be changed to resolve the confusion about this mysterious "Setup."
The issue arose because what I thought was going to be eth0 was actually not. It turned out to be eth2, after moving the cable to interface eth0 everything worked fine. The issue is that there was no setup in the console allowing the user to select which interface would be the green interface, it just assumed that it was going to be eth0.
I found that I was able to re-order the interfaces using the command ethconfig and it's configuration file /etc/businfotab
# Generated by ethconfig
eth0 00:02.0
eth1 02:04.1
eth2 02:04.0
eth3 02:02.1
eth4 02:02.0
eth5 03:00.0
eth6 03:00.1
The numbers to the right of the eth designations are the PCI Bus Addresses of the interfaces. Re ordering the PCI Bus Addresses and appropriately naming them to the desired eth designations will result in the eth interfaces ordering properly on the next reboot.