The Ensembl API docs and tutorial describe a HomologyAdaptor class which has a fetch_all_by_MethodLinkSpeciesSet_orthology_type_subtype method. However, I'm pretty sure that the adaptor you are using is a MethodLinkSpeciesSetAdaptor, which doesn't inherit from HomologyAdaptor. This is just a guess, but what happens if you change this:

my $homology_adaptor =
        $reg->get_adaptor ('Multi', 'compara', 'MethodLinkSpeciesSet')
+;
[download]

to this:

my $homology_adaptor =
        $reg->get_adaptor ('Multi', 'compara', 'Homology');
[download]

?

Cheers,

Tim