You can extract first 512 bytes from each hard drive and compare them.
This two lines
dd if=/dev/sda of=/tmp/bootsectorSDA.txt bs=512 count=1
dd if=/dev/sdb of=/tmp/bootsectorSDB.txt bs=512 count=1
will produce two files /tmp/bootsectorSDA.txt and /tmp/bootsectorSDB.txt - you can compare them. If they are different then probably you don't have MBR on second hard drive.