Description
If you set the number of lanes to 2 for the IP Compiler for PCI Express, the PCIe core clock frequency would be displayed as 12.5MHz at the Clock Settings tab of Qsys GUI.
Resolution
To get around this issue, you can modify line#1503 of pcie_parameters_validation.tcl in (<Quartus II installation directory>\ip\altera\altera_pcie\altera_pcie_avmm)
From:
set_parameter_value core_clk_freq 125
To:
set_parameter_value core_clk_freq 1250