The SP605 Schematics indicate that settings are such that F_SEL1 = 0 and F_SEL0 = 1, which defines oscillator output is 125 MHz clock. The data sheet for this part (
http://www.xilinx.com/products/boards/ml510/datasheets/ics874001.pdf) indicates the same. The net name is a misnomer, 250 MHz is not an option, but the functionality is still as expected by the reference designs shipped with the kit.
This article is to confirm that PCIE_250M_N / PCIE_250M_P pair supports 125 MHz on the SP605.