I had problems with boot speed where booting W2k, it would sit at the longest time at the middle of the blue boxes. I was installing a secondary drive in which it was giving me warnings about it being bad so I disabled the hardware check option. (Sorry I can't remember the screen or the option name but it would basically allow stop of boot on failure of keyboard etc)
After disabling, it boots fast. I have yet tried to go back and turn it back on to see if it was causing the problem but you might want to try it.