“Duplicate” Posts Appearing Since 3.1.2 Update

are you using global $query_string; before the query?
so that the full line looks like: 

<?php global $query_string; query_posts($query_string . '&cat=-10,-12'); ?>

alternatively, you could try: 

<?php query_posts('cat=-10,-12&paged='.get_query_var('paged')); ?>

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