This should do it:
DELETE t1 FROM wp_postmeta t1, wp_postmeta t2
WHERE t1.meta_id > t2.meta_id
AND t1.meta_key = t2.meta_key
AND t1.post_id = t2.post_id
This should do it:
DELETE t1 FROM wp_postmeta t1, wp_postmeta t2
WHERE t1.meta_id > t2.meta_id
AND t1.meta_key = t2.meta_key
AND t1.post_id = t2.post_id