maybeD,
There are many ways of trouble shooting weird mysterious problems. Sprinkling print statements everywhere is often a favorite (have you verified the hashes are correct before you return them?). One that I often reach for is starting with a known quantity and add pieces gradually until it stops behaving as I would expect. So, that is what I suggest here:

#!/usr/bin/perl
use strict;
use warnings;

my ($href1, $href2) = gen_hrefs();

sub gen_hrefs {
    my %h1 = (one => 1, two => 2, three => 3);
    my %h2 = map {$_ => ord($_) } 'a' .. 'z';
    return (\%h1, \%h2);
}
[download]

Once you see that does exactly as you expect, modify it little by little to look like your actual code and see where it breaks.