I got a solution
This happenes to one of my WD Caviar 18gig drives. My speculation is taht the HDD needs more time to be recognized, so the first boot the MotherBoard doesnt recognize it but a reset and the drive is dectected the second time around. If this is your problem here is what i did:
Solution 1) YOu can increas your HDD delay to let the HDD powerup and do whatever it has to to be dectedin your system, you can access this in your MoBo BIOS.. the value should be in seconds, and you should increase it to whatever value it need to be properly recognized
Solution2) Goto your bios, and hve teh HDD autodected, then set the drive as manual with the dected values. What will happen is the MB on bootup will not scan that IDE device, but instead will assign the values that were in the manual values, not only giving you a faster bootup but avoiding reboots.
YOur milage may vary depending on your MoBo and its flexibility, any new motherboard should be able to do both of these functions, if you have the drive on a raid card, you might have to move it to IDE 0 or 1 so you can do the tweaking in your BIOS
GL, hope this helps