Sean,
Just to clarify. The PHY module will not link if connected to a 10MB or 100 MB infrastructure as the PHY module only supports gigabit speed.
Also, the layout of the ports on the module are
9 - 7 - 5 - 3 - 1
10 - 8 - 6 - 4 - 2
Just to make sure you were actually connecting to port 1.