They have the same dates apart from boot.ini, the original is from 14/10/2006, the copy 11/10/2006. The only changes which have been made to the server recently was installing Critical Update for Windows Small Business Server 2003: Vista and Outlook 2007 compatibility (KB 926505)
D drive is used just for backing up. I use Acronis True Image. This night one of its service crushed and the backup wasn’t made.