When it does something like that (show the last 9 no matter what), usually that means something's defaulting, somewhere. Does the plugin specify whether the 'name' is the slug or the actual name? Whichever you're using, did you try the other? Like, category name (seen by user) may be "cross country skiing" but the slug is ski_xctry.
But if all you want is to show posts in category 1 in one section/column on the front page, and posts from category 2 in a another section, why not just tweak the front page's code a little?
ie, in section one:
<?php $feature_post = get_posts( 'category=39&numberposts=4' ); ?>
<?php foreach( $feature_post as $post ) : setup_postdata( $post ); ?>
[continuing with rest of usual loop for posts]
that shows the last four posts in category #39. then do it again for the next section you want to display:
and so on.