Problem with Home Page

Hello WPMU Team,

I'm using Membership 3.2 on a WP 3.3.2 MU Installation with the Theme mysitemyway inFocus.

On the Home Page the_content of all Membership Pages are being displayed. The Theme is setup to add the_content of a certain Page to the Home Page. To do that a WP_Query object is created with a post__in Argument set to the specified Page-ID.
It only seems to happen on the Home Page, that the Membership Page contents are also being displayed.

Some Code...
The Part of the Theme which is involved:
$content = mysite_get_setting( 'mainpage_content' );

if( $content ){
$args = array( 'post_type'=>'page', 'post__in' => array( $content ) );

$my_query = new WP_Query( $args );
// if(isset($_GET['DEBUG']))
// var_dump($content);
if ( $my_query->have_posts() ) {
global $more;
while ( $my_query->have_posts() ) {
$my_query->the_post();
echo '<div class="' . join( ' ', get_post_class( 'page' ) ) . '">';
$more = 0;
the_content();
echo '</div>';
}
}

The WP_Query object/result $my-query is altered by the ensure_option_pages_visible() function in membership\membershipincludes\classes\membershippublic.php

I don't want to change the code of neither the theme nor Membership Plugin. Can you think of a solution to solve this incompatibility? Furthermore I don't quite understand why the WP-Query Parameter post__in is always being altered by the function ensure_option_pages_visible()?

Cheers
Julian