foreach(@suffix) {
                $sf = $_ ;

                print STDERR "$mn $sd $sf\n" ;

                # Build the filename of the data file we want
                $fn = "$sd/data." . $sf ;

                open(DATA, "<$fn") || print "Failed to open $fn\n" ;

                # Store the data in a multidimensional hash (this will
+ overwrite
+ the hash, but that's
                # not the problem with this bug.

                while(<DATA>) {
                    $v{$mn}{$sd}{$sf} = $_ ;
                }
....
[download]

See the foreach at the top? It's storing data in $_. Then you're using $_ in your while loop also. The second is stomping on what's in the first. Do a

 
while ($foo = <DATA>) {
    $v{$mn}{$sd}{$sf} = $foo;
}
[download]

At least that's what grabbed my attention first.

Rich