I'm not sure exactly what you are saying or asking.
Do something for me and I'll be better able to understand your situation:
Type the following into the Run box (just do "Windows Key + R" on the keyboard for the shortcut to it) and hit Enter:
Maximize this "Disk Management" window and take a screenshot using the "Prnt Scrn" button on the keyboard. Paste this into Paint, save it, upload it to the internet, and post it here.
Disk Management can speak loads for what is going on in a system better than most people can.
Also, try to explain your problem better. I couldn't understand exactly what your problem is. Something about the OS looking in the wrong place or something. Use the names in Disk Management to refer to what partition, hdd, etc... that you are talking about. Do you have one hard drive with multiple partitions? Or separate hard drives? I don't know what you want to "fix" because I don't know what the problem is. I can most likely fix your problem once I know what it is.
Spell it out for me very plainly, and I'll do my very best to help you.