The example design that is generated by the Spartan-6 FPGA GTP Transceiver Wizard automatically includes ChipScope tool ILA cores that can be used to observe the behavior of the design in hardware. This Answer Record contains information on errant behavior that might be observed when generated by v1.3 of the Wizard.
When implemented in hardware, it is possible that the ILA will report a couple of cycles of valid data followed by zeros. This is a known issue with the design and does not reflect on the functionality of a user's ChipScope software installation. This issue is scheduled to be corrected in a future version of the Wizard.
This does not preclude the generation of custom ILA cores or their use with the example design.