SD card read sector problem
What you read om the µC is the MBR (Master Boot Record) with the partition table. This data you cannot read on a OS like windows without admin privileges! The USB card reader data clearly shows the first sector of the "drive" (partiton)- which is not sector 0 (zero). 

Some hex editors can show your the MBR if started as an admin - but you must use the correct physical device, which has no drive letter.