There is a known issue with the Spartan-6 FPGA GTP IBERT core in 13.3, 13.4, and 14.1.This answer recorddiscusses the issue in detail.
The Spartan-6 FPGA GTP IBERT core in 13.3, 13.4, and 14.1does not show the correct line rate when the transceiver is set to 2.5 Gbps. Instead, the IBERT core shows a line rate of 2.042 Gbps. This should not cause an issue with evaluating the transceivers in the Spartan-6 device, since it is actually running at 2.5G. This only affects the link status rate shown in the interface. This issue is to be addressed in version 14.2 of the tools.