There is a reset circuit on the that controls the complicated power sequencing. It is possible that your BIOS is too fast and configures the PCI space during this powerup sequence. At that time, the HDE is not properly accessible.
It is possible to shorten this sequence a bit, but for that you need to exchange a SMD capacitor on the HDE board.
OK, thanks. I have the "Quick Power On Self Test" enabled, so by disabling this I should have this problem fixed.
Josce