use strict;
use warnings;

my %active_modules = (
    'clouds'    => sub { CloudUpdate::cloud_update() },
    'volcanoes' => sub { VolcanoXML::process_volcano_data() },
    );

process_modules(\%active_modules);


sub process_modules {
    my ($active_modules_ref) = @_;  # Accept %active_modules as a refe
+rence

    print join "\n", keys %$active_modules_ref;
}
[download]

prints the hash keys as I would expect. What is different with your code? Maybe you could simplify your code to a similar test script to demonstrate the problem?