How Can the System Drive Become a Different Than The Boot Drive?

I am attempting to create a system image I can use to restore Windows 7 so I don't have to keep reinstalling Windows and all my software to use a fresh system. In the Create a System Image options I noticed that I could not uncheck the D: drive, which I use for storage only. Then I went to Disk Management and found that while the C: drive is the boot drive, the D: drive is the system drive. When I unplugged the D: drive, Windows would not boot. Right now I am attempting to repair the C: drive for startup with a Windows 7 Repair Disc.

Any thoughts on how this can happen?

The easiest way for this to happen is when a previous OS was on the second drive before win7 was installed.

win7 will write it's boot (system) files to an existing active drive or partition if one exists,at the time of installation.

this often happens with win7 when "upgrading" from XP when a new install is actually required

There has never been an OS on the D: drive, it has always been a storage drive only.
I thought you could not upgrade, only do a clean install if coming from XP because the architecture is different and that you could only upgrade from Vista?

My startup repair attempts are unsuccessful so far. The startup repair claims to have succeeded saying that the problem is "The partition table does not have a valid system partition." Any thoughts?

Please post back a screenshot of your full Disk Management drive map and listings, using Snipping Tool in Start Menu - attach file using paper clip in Reply Box.

It may be that you only need to mark Win7 active to get Startup Repair to work after a few attempts. You can deactivate D at the same time.

But we need to see the screenshot to be sure of the steps and avoid unintended consequences.