You may want to check that your PIO and DMA modes are set correctly.
Read this:
http://www.pcguide.com/ref/hdd/if/ide/modesPIO-c.html
edit: Just read your second post. You must not have your boot drive setup as master. You want to set the jumper on your existing drive as master and the jumper on the new drive as slave. I can't remember the cable placement either as I haven't messed with that in a while.
Another option is to connect you new drive to the second IDE bus, then you don't have to mess with jumpers.