My Windows installation is on 2 Drives...strange problems

Ok, so basically, it seems that I have 2 installations of windows. One on my D drive, one on my C drive. (By the way, this wasn't my computer until recently.)

Anyways, if I go into the C drive, it has a WINDOWS folder, and if I go into that, it has a system32 and all the important system files.

In my D drive, there is also a WINDOWS folder, however it has less files than the one in my C drive, however, if I go into the WINDOWS folder in either drive, and then into system32, they both have the same amount of files.

So basically, this is screwing me up. Because, all the commands in CMD do not work.

For example, you know the command net user, which shows all the users on your computer? If i type this in, all it shows is Administrator and Guest.
And yeah, neither of these are users on my computer.

So that's just an example of what doesn't work, I'm sure you could fathom all the rest of the system commands i can't do because it can't find any system paths or anything to do with windows.

Can anyone shed some light on this and help me fix it?

 

Ok so, then what is the problem with my computer? How come it doesn't seem to recognize my windows installation?