I had this problem as well. My main hard drive wasn't being recognized until I hit reset and then the system would recognize it and come up just fine.
Wasn't until like 2 weeks ago I swapped out the high speed fans in my case for some nice, quiet Vantec ones. Lo and behold! Suddenly the system boots on the first try everytime! I had 2 hard drives and 2 fans running off the same lead out of the power supply, the new setup has 2 hard drives and 1 fan running off the same lead, with the other fan running off the motherboard lead. Perhaps it was simply too much powerdrain upon bootup with all that connected to the same wire?
Try swapping some components to a different wire that are sharing your hard drive(s) power leads, or temporarily disabling a case fan or 2 and see if it boots on the first try. Maybe it'll work for you too? Worth a try...
FluxCapacitor