I think there is a bug in the ID query regarding the LIMIT calculations. If your post count setting is > 500, the limit computation is wrong.
To fix the problem, in main.php in the collect_ids() after this:
$limit = explode(',', $query); $start = (int) $limit; $finish = (int) $limit;
add this line:
if($finish - $start > $count) $count = $finish - $start;
to increase $count eventually.