Можно найти некоторые полезные инструменты здесь: http://support.microsoft.com/default.aspx/kb/231282/en
the compact PCI backplane is passive: the PCI bus is driven by the CPU board. obviously, your new CPU board does not enumerate the PCI bus in the same order than the old board, thus BAR 2 and BAR 3 are switched... however, i have no idea how to correct this.