The work-around for this is as follows:
1. Click on "Add External Port" to create an external port.
2. Then, in the net column, XPS will show you all the possible net names.
3. Choose the existing net name which is connected to the CLKOUT port.
This problem has been fixed in EDK 11.4, available at:
http://www.xilinx.com/support/download/index.htm