PCIe negotiated as x1 instead of x8

Thanks for the prompt reply. The kit I am using is: http://www.altera.com/products/devkits/altera/kit-pciexpress_s2gx.html. On it, pin A1 is PCIE_PRSNT1n, pin B48 is PCIE_PRSNT2n (internal signal: PRSNT2_N_X8), and pin A11 is PCIE_PERSTn. The remaining 2 internal signals, PRSNT2_N_X1 and PRSNT2_N_X4, are mapped to pins B17 and B31 respectively, which are left floating.

According to the board schematics, pin A1 and B48 are connected together via a 0 ohm resistor (R43). I have verified it using a multimeter (approx 0.7 ohms). Do you mean I need to conenct PCIE_PERSTn (A11) to B48? I do not see any jumper on the board which allows me to do that.