Xilinx Pci Express core and Nital board Issue

I have a query regarding the Nital PExBuilder-X254-pci express X4 Xilinx design kit which uses xilinx Pci express logicore version 2.1. Presently the board is being tested with Supermicro X6DH8-G2 motherboard which has 8x and one 4x(8x slot mechanical and 4x electrical).

I found that sometimes the board is being configured as 1x instead of

4x. This problem is quite random.Approx once in twenty times i.e if i reboot the machine twenty times the board may configure to 1x once. if anybody else has faced similar problem, can u please give some pointers

regarding the problem I am facing.

Thanks, Sarun