The services module limits the amount of taxonomy vocabularies and taxonomy terms it shows to 20 by default.
This is how you can configure it to serve more vocabularies/terms:
For Drupal 6 add this to the database:
for terms:
insert into variable VALUES ('services_taxonomy_term_index_page_size', 'i:200;');
for vocabularies:
insert into variable VALUES ('services_taxonomy_vocabulary_index_page_size', 'i:100;');
For Drupal 7 it's easier: add this to the settings.php file
for terms:
$conf['services_taxonomy_term_index_page_size'] = 200;
for vocabularies:
$conf['services_taxonomy_vocabulary_index_page_size'] = 200;
After this restart your webserver (D7 only) and clear cache to see the change.