This is a known issue for 13.2. For the Kintex-7 GTX IBERT core, the TXOUT_DIV and RXOUT_DIV attributes are set incorrectly to a value of 1.
To work around the issue, click on the DRP tab with the IBERT core up in ChipScope Analyzer and find the TXOUT_DIV and RXOUT_DIV attributes. Change both of these attributes to 2 and press enter. This changes the attribute using DRP and your line rate should now show 3.125 Gbps.
This will be fixed in 13.3.