the last time I used this, the phy controller provided debug info. for example, the state machine will always pass stage one and two, but will fail at the first IC to have issues in phase three. This might be due to a soldering defect if this is a custom PCB. It may also be due to a timing issue if you don't provide the correct timing contstraints. It can also be due to settings issues. In anycase, determining the exact point of failure, or at least the first point of failure, might be useful.