It seems to me that your trying to store a list as a hash, so when you print out $m you only get one item, the first item, since that is the key of your hash. If you change it to an array you get both items.

my @list = (
        [
            "'NEIS.IFMS.CP2#LOAD.CHGT.DAT'" => 0,
            "sqlload / ifmschgt.dat >> ifmschgt.log" => 0
        ],
        [
            "'NEIS.IFMS.CP2#LOAD.TOLT.DAT'" => 0,
            "sqlload / ifmstolt.dat >> ifmstolt.log" => 0
        ],
);

store( \@list, 'store' );
my $root = retrieve( 'store' );

foreach my $line ( @{ $root } ) {
    foreach my $m ( @{ $line } ) {
        print $m, "\n";
    }
}
[download]

HTH