On my small home page I'm getting in certain custom publish types by using this:

<?php $loop = new WP_Query( array( 'post_type' => 'news', 'posts_per_page' => 4 ) ); ?>
<?php while ( $loop->have_posts() ) : $loop->the_post(); ?>
etc....

This works fine. However Among the finest to usher in a listing of blogs using the default taxonomy. And So I do this:

<?php query_posts( 'cat=uncategorized' );?>
<?php if ( have_posts() ) while ( have_posts() ) : the_post(); ?>

Also it spits out all of the custom publish types, although not the main one blog publish I've (the hello world blog publish). I seem like I've carried this out before with no problems, but can't evaluate which I'm doing wrong.

I believe cat it's combined with category id, for the reason that situation could be query_posts('cat=1') If you wish to make use of the title try ('category_title=whatever')

Hope its helpful GL

Have you got wp_reset_query a spot after the first query and prior to the place where you are attempting to bring that list?