The most common side affect of disabling auto-negotiate on your CityLink facing interface will be a duplex mismatch. In this situation the CityLink equipment believes the link is half-duplex while your equipment believes it is running at full-duplex. The duplex mismatch will cause packet loss and poor performance.
If you are unable to use auto-negotiate on your equipment please contact CityLink to discuss your requirements (tech@citylink.co.nz).