Heureka! I found a soultion for the pagination on the Site5-supportforum. The Since the supportforum is not accessible for noncustomers i'll post it here:

In home.php, after the comment <!-- End #featuredPosts -->, comment out from 
"if(!query_posts('showposts=.... to the latest } 
until before
"if (have_posts()) : while (have_posts()) : the_post(); ?>

And then, at the end of the page, after wp_reset_query();?>, add these lines: 

<div style="clear:both;"></div>
<?php if (function_exists('wp_pagenavi') ) {
wp_pagenavi();
}?>
</div>

What it does is: It ignores the number of posts to show that you have set in the themesettings. Instead login in you admin page, go to Settings -> reading and limit the numer of posts there to the amount you wish.
You might need to clear the cache. Thats it.