well this might be the case that, when the system drive ( C:\ ) is unattainable, windows was unable to install or modify system files there and so it opted for drive D, when prompted to quick format, what actually got quick formatted was D and not C as expected.This happens when there's a corrupted OS on C: and u want to quick format it and load windows.
Best way is to format C: using floppy boot and then install windows on fresh formatted C and not on remanant C:
Lest u can do now is format both C: and D: using floppy boot and then install a frsh copy of windows to C: