I think you want to be constructing a new Digest::MD5 object for each file, not reusing the same one. Otherwise you'll get a cumulative digest.

I strongly suggest looking at Path::Class which makes working with files and directories a lot easier, reducing a lot of "boilerplate" code.

use Digest::MD5 ();
use Path::Class ();

sub ScanDir
{
    Path::Class::Dir::->new(shift)->recurse(callback => sub
    {
        my $file = shift;
        return if $file->is_dir;
        
        my $stat = $file->stat;
        printf(
            "%s, %s, %s, %s, %s\n",
            $file->absolute,
            $stat->size,
            $stat->atime,
            $stat->mtime,
            Digest::MD5::->new->addfile($file->openr)->hexdigest,
        );
    })
}

ScanDir("/tmp");
[download]

Path::Class::Rule is also good fun, though not especially useful for this particular task.