Is the folder you cannot delete on the C or D drive? If on the C drive, and it's the old My Documents folder, then there's a fair chance that some program is still using that space as a storage location, and thereby preventing it from being deleted. How did you move the folder to D in the first place? Best method is to right-click on the 'my documents' icon on the desktop and check which folder it points to. If that still says C: then change this to the right location, and when windows ask you if you want to move everything over click 'yes'.
As for the missing space, do you have Norton Systemworks running? Or something similar which protects deleted files?