I have a strange issue on an early 2008 Mac Pro running OS 10.6:

• if I restart the computer it restarts normally
• if I shutdown and boot, it stops at the grey screen just before the boot process
• if I shutdown and boot but hold down the option key, I can select the boot disk and all is good.

I've just cloned the disk, and the same thing happens.

• The disk is a SAMSUNG HD154UI
• The disk is partitioned (the second partition holds a clone of the Snow Leopard Install disk)

One weird thing on the original disk was one of the partitions said 'EFI Boot' in a non-aliased font rather than the name of the disk when the disks are listed upon holding down option.

Solution: it seems that there was a problem with the disk. Part of the difficulty in finding the solution was that you need to remove the disk from the computer completely. For example, a good disk in Bay 3, wouldn't boot up if the bad disk was in Bay 2. So for ages I thought the problem was hardware related in Bay 3. So if you think you have a dodgy disk remove it totally if you are testing the hardware with a 'clean' disk. Cleaning the PRAM helped to get the new disk to work too.