Windows 7 backup shows two system drives

I had this same problem, both the C and D drive were required when doing a Windows 7 image backup. I felt it was not necessary to include the D: drive in the image backup.

I have always used the D drive when possible when I installed software. Since I switched to a SSD using D drive became more important (120GB SSD). I found 3 services that pointed to my D drive. I switched two of the programs from the D to the C drive. The third, which is photo editing software, I had already marked as disabled. I deleted the service in the registry in HKEY_LOCAL_MACHINE\SYSTEM\CurrentControlSet\Services\

I solved my problem but in a very long and arduous way.

After I found that Windows was booting from the D: drive by disconnecting it, I first ran cmd as Administrator and used the BCDBOOT tool. I typed:

bcdboot c:\windows /s c:

I then tired to use diskpart while in Windows to clean the drive but it wouldn't allow me too. So I booted into Windows repair section with a Win7 recovery disk (similiary to what @justakid suggested) but instead of doing the automatic fix I opened cmd in recovery mode. Oncein cmd I used diskpart to clean the D: drive of boot files by:

DiskPark
Select Disk 0 \\my D: drive
clean

I then rebooted and the D: drive was no longer a System drive.