The only thing that matters is what Windows version is being used to enumerate the PnP device. (You could have a blank drive, or a previous LINUX drive, or a Win2k drive).
As a clean install using Win2k, the article suggests that there is something wrong with either your jumper setting, or the cable connection.
Check that your older or new drive (particularly if Western Digital) does not require an additional jumper for a second drive in a two-drive configuration.
For IDE devices you have nowadays a choice between the traditional Master/Slave, or Cable Select. Cable Select is the most often seen on newer motherboards, controllers and attached hard disks. But you cannot mix them. As a guess, even if set to "Master" the new drive needs to be set to cable select, as well as the newer drive you are adding. And with a Cable Select type of cable, you need to be sure drive 1 is at the very end, and drive 2 on the middle of cable connector.