The problem is that when you partitioned that drive, you created a primary and an extended partition. What happens is that when your system is booting up, it looks through the IDE channels for primary dos partitions. It finds the one on your primary IDE, assigns it drive letter C, then goes through the rest of the channels and assigns your slave drive primary dos partition drive letter D. It repeats the process with logical drives on the hard drives.
To resolve this, you need to delete all partitions off of the second drive that you just set up. Then you need to create only an extended dos partition on that drive, then create your logical partitions on that extended partition