hard drive ghost

I made a backup (total mirror) of a drive to back it up
and after the backup checked that the used disk space on
both hard drives were the same, and not checking that all
the files were really there.

after the format copied the data that i wanted over, just
simple pictures and documents, all the documents were
there but half or only a few of the pictures were there.

they have disapeared,
before this i had copied data from one drive to another,
shut down the computer removed the hard drive i had
copied from and then restarted the machine, and all the
data i had copied was gone, but the file space was used
up.

can anybody explain or help me with this?

thanks
Matthew