Position??? Um. No. Position is only important if you set your drives with a jumper using the "cable select" option. This can work, in theory. In practice for the empeg, I have always found it easier to set it by using a jumper to set a drive to slave, no jumper to set a drive as master. The position of the jumper on the drive may be different for different manufacturers and models.

This is certainly a master drive, with a fully bootable image on it. Okay. Does it have any jumpers on it? If so, remove it. This should force it as master.

Now, about that 12GB and 40GB - did either have jumpers on them when you were testing? Based on your posted logs, I am not sure it will matter. The 40GB did not respond to the probe and the 12GB seemed to lock up the boot cycle.