Had just fix a similar issue. Ran a crossed this post looking for ideas. This is what I did and it worked.
Disconnect sata cable to hard drive with operating system.
Put windows 7 install disc in cd rom.
With new hard drive connected power up your system.
Run windows 7 install till it gets to the part where it will show you the hard drive and allocated space.
Proceed to install the first part of windows 7 install.
I let it run till it said 7% then cancelled the install. Remove install disc. Then shut down the system.
Reconnect hard drive with operating system. If system does not boot and request disc, shut down and switch sata cables.
Once system has booted go to START then COMPUTER.
Hopefully you will see the 2 hard drives.
Right click on new hard drive and select format.
Hope this helps.. my first post.