I encountered this issue today and even though I am a 15 year IT veteran, in my haste I re-installed Windows without looking for a solution first:
After a fresh installation of Windows 7 Professional everything seemed fine, I updated all the drivers put my favorite utilities back in and then saw that I left the Windows install DVD in the drive.. I removed it and then restarted after more updates and I got an error that Windows could not boot and I should run the repair tool from the disk..
I restarted the computer with the install DVD in the drive, got distracted and missed the opportunity to press any key to boot the dvd.. however Windows booted!! I thought that was weird, and too good to be true.. I removed the DVD rebooted and tried again… FAIL!!
So…. Like a DOPE… I re-installed Windows 7 all over again thinking something was corrupt and BAM!!! same damned problem… so finally I put the disk back in the drive, booted and Googled “Windows will not boot without” and up pops “Windows will not boot without the install DVD” Selected that and the rest is history!
All I had to do to fix it was to change the SATA cable order on my hard drives. The boot hard drive was plugged into Sata port 1 and my data drive was plugged into Sata port 0…
Swapped the two, removed the Windows & install DVD and booted just fine! ALSO this same thing happened to me on another computer and I ran EasyBCD which is FREE and then found that for some reason the boot drive was set to D so I changed it to C and rebooted and everything worked fine.
Hope this helps someone!