List of filtered Events is breaking paging?

You have two queries that look to me to be competing.

1. You are using query_posts to alter the main query but are not including any of your filters in that one.
2. You are creating a new query with your filters– 'meta_key' => 'start_date', etc– and looping over that query result set to show your posts.
3. Then to paginate you using the main query– $wp_query— which doesn’t have any of your filtering. It isn’t surprising that things are out of sync.

You need to re-factor this to only use one query and not jumble the two together. I believe you can use the $loop object just as you are using $wp_query in the pagination function.

function paginate($loop) {
  global $wp_rewrite;
  $loop->query_vars['paged'] > 1 ? $current = $loop->query_vars['paged'] :   $current = 1;
  $pagination = array(
    'base' => @add_query_arg('page','%#%'),
    'format' => '',
    'total' => $loop->max_num_pages,
    'current' => $current,
    'show_all' => true,
    'type' => 'plain'
  );
  // ...

I can’t promise that that is a complete solution. What you have got is complicated and difficult to test without duplicating your database and page structure.

It is also possible that you could use a pre_get_posts filter to alter the main query and save the database some pain.