Rolli59 is correct, but let me throw in a little more detail.
If you install any version of Windows on an empty drive while another drive that has a bootable Windows OS on it, it will use the other drive's boot sector. If you install Win7 on an empty drive with another empty drive on the system, it will build a 100 MB boot/recovery partition on the second drive and your system will actually boot from the second drive. Microsoft considers this a safety feature.
So the system drive must be the only drive connected to the system when you install Win7.