Why is the RX/TXPCSHCLKOUT not working in hardware?
This is a known software issue and is addressed in ISE 7.1i Service Pack 3.
If using ISE 7.1i Service Pack 2, the RX/TXPCSHCLKOUT signals can be used by instantiating the MGTB in a tile.
MGTBs have even Y co-ordinates:
e.g. XxY0, XxY2 etc.