So the solution after much cursing and pulling of hair was to ditch the WP_Query and go with get_posts instead, while referencing post_title
like so:
<div class="my_meta_control">
<p>Add or subtract Athena projects related to this project.</p>
<label>Available Projects</label><br/>
<?php
$args = array('post_type' => 'athena_project', 'posts_per_page' => 1000);
$items = get_posts($args);
$mb->the_field('item', WPALCHEMY_FIELD_HINT_CHECKBOX_MULTI);
foreach ($items as $item) { ?>
<input type="checkbox" name="<?php $mb->the_name(); ?>" value="<?php echo $item->post_title; ?>" <?php $mb->the_checkbox_state($item->post_title); ?> /><?php echo $item->post_title; ?><br />
<?php } ?>
<br />
<input type="submit" class="button-primary" name="save" value="Save" />
</div>
Now everything works beautifully.