Sorry – this is probably an obvious answer but without seeing your query_posts query it’s hard to say if you’ve tried this or not. As you’re altering the main query on the page query_posts should be the right tool for the job.
Something like the following query should work:
<?php query_posts( 'posts_per_page=100' ); ?>
<?php if (have_posts()) : ?>
// Something before posts display
<?php while (have_posts()) : the_post(); ?>
// Post Content
<?php endwhile; ?>
// Something after the loop
<?php else: ?>
// Something in case there are no posts
<?php endif;?>
If you’ve already tried this can you edit your answer to show the code you’re using? Also are you using any custom taxonomy templates or are all taxonomies going through taxonomy.php?