That sucks Man
I'm always parinoid about this happening. Not to make you feel worse but in the future it's a good idea to copy files to the new drive, test the MD5, and then recopy the files if necessary, and backup, backup, backup. You never know when the drive could fail.
Are you sure you are not missing one of the SHN files? The MD5 will fail if 1 or more of the files is missing?
I don't know exactly what causes this but it can happen.
Joe