2nd HDisk (D:) not visible after restart

I've just upgraded from Windows Xp to Vista sp2 in a computer with two hard drives , the 1st ( C: is connected to IDE of motherboard and the 2nd ( D: is connected to a PCI_IDE Controller ( Silicon Image Sil0680 ATA/133 controller).When I start my system loads the Windows Vista in a minimum time(1.5min) and everything is operating fine including Device Manager where " all devices are working properly " and " all drivers are the best existing " but when I restart the computer then after reading BIOS the screen remains dark more then 6 minutes and the hard drive's C: led is off . Finally, after loading the operating system everything is ok , except that I don't see the 2nd hard drive ( D: that is connected to PCI_IDE contoller although in Device Manager in category Storage Controllers the controller seems working properly and the driver too. This doesn't happen on a normal start (after shutdown) that everything ( Hardware and Software ) is working fine . Would a new upgrade (Repair) over the existing one solve the problem ? Any help appreciated.

Since it's a new install you have to re-install the PCI/IDE controller card drivers...