I’m not sure if this is a problem with the query or a bug. To narrow it down, could you try the following:
1. Deactivate all of your other plugins and switch to the 2012 theme for a moment. Does the full query work? If so, a plugin or the theme is interfering with the WordPress query.
2. Add the code below to your theme file to check the query results without using MapPress. If they are still incorrect, there is a WordPress bug or something is wrong with the query itself:
<?php $wpq = new WP_Query('category_name=lachlan-catchment,rivers-creeks&post_type=events&meta_key=event_end_date&meta_value=20130618&meta_compare=<'); print_r($wpq); ?>
If the results for #2 are correct, then it’s a bug in MapPress and I’ll be happy to trace it for you – please send me an email with the contact form and provide an administrator login to the blog.