Another way to fix this is to disable checking floppies on shutdown in your antivirus program. (incase someone else has this problem too)

Is your second hard drive new? Did you format it yet? If not, you can use the maxtor utility that came on the cd with the drive to format it. You should see it then.

if they are on seperate channels, the cdrom should be set to master as well as the hard drive. The master/slave option is only really used for items allong the same ide cable. If this does not fix...

Just plug in the new sata drive, and double check the bios settings to make sure that the boot order checks your old hard drive for the master boot record and that it is not checking the new sata...