it may be a matter of file fragmentation or links
I use a snapshot approach - see rsync snapshot backups
using cp -al and a bit of renaming. I had to use the modify-window option to handle an CIFS problem.
If you are thinking of writing scripts, I'd consider calculating md5 sums. Remasterys does this with
find . -type f -print0 | xargs -0 md5sum > md5sum.txt
(that's a script to create a bootable DVD backup for an Ubuntu system). You can run this on both systems and then analyze the resulting md5sum lists for errors.