EDIT2: I have been told that in my case, the dual boot setup meant that my old windows hard drive held critical information for booting and operating my win7 hard drive. If this is the case, what can I do?
That';s exactly what happened. If you want a seperate OS installed without mutli-boot, always disconnect all drives except the one you want the OS installed on.
You might be able to fix it with a repair install, otherwise follow these directions. http://support.microsoft.com/kb/927392
Worst case, you can always disconnect all drives except the one you want to boot from and reinstall windows onto it. Do a custom install so that you get the option to delete all old partitions if you want/need to.