When running an IPI design through Implementation, the following message is received:
The correct pin sites had been selected to connect a REFCLK with a GT, so why would the constraints not be applied?
In this case, an IPI utility buffer was used to connect the top level pins to a PCIe block containing the GT that the pins were connected to.
However, the wrong buffer was used as "IBUFDS" was selected instead of the "IBUFDS_GTE2" required by the GT.
Changing this to the correct buffer and resynthesizing resolves the issue.