Tim wrote:
Conversely, you can opt to jumper your drives as master and slave, and it doesn't matter whether you connect the drives to the master or slave connectors. All those connectors do is open and short a pin on each drive, just the same as putting in jumpers on the extra header does.
AFAIK, the jumpers also select whether or not the drive uses terminators. The master has the terminators and the slave does not. The terminators must be at the end of the cable or reflections may occur. At higher speeds these reflections are important.