Sedrick, Please check the volumes, those should be clean, attached to the Windows box. Check the <b>chkdsk</b> is running? That could be one possibility for the long boot time. Try rebooting the server again to see whether every boot takes the same long time like 45 min to 1 hour or this is the first time it tool such a long time. What is the ram status, is it enough?
Do update us again.