[U-Boot] ppc4xx: u-boot sees PCIe endpoint, linux does not.

Hello,

AMCC PPC460EX canyonlands board with an FPGA PCIe end point:

u-boot sees the end point, but Linux does not:

U-Boot 1.3.3-00249-ga524e11 (Jun 30 2008 - 16:05:51) CPU: AMCC PowerPC 460EX Rev. A at 800 MHz (PLB=200, OPB=100, EBC=100 MHz) <...> Board: Canyonlands - AMCC PPC460EX Evaluation Board, 2*PCIe, Rev. 16 <...> PCIE1: successfully set as root-complex 02 00 2071 2071 00ff 00

Now, if I re-program the end-point FPGA during the u-boot boot time-out, Linux will recognize the end-point.

Any takers on what I should start looking for?

Regards,