I figured out how to fix it, but you'll have to edit the "search-everything.php" plugin file to do so.
On line 257, replace this:
add_filter('posts_search', array(&$this, 'se_search_where'));
add_filter('posts_search', array(&$this, 'se_search_where'),10,2);
Then, on line 341, replace the following code at the top of the se_search_where function:
global $wp_query, $wpdb;
function se_search_where($where, $wp_query)
if ( $GLOBALS['wp_query'] !== $wp_query )
What this does is say, "If this isn't the same query created by Search Everything, don't add the Search Everything "where" clause to the query."