Using tuples in a WHERE clause can cause a MySQL slowdown. Consider:


UPDATE tbl SET col=1 WHERE (pk1, pk2, pk3) IN (1,2,3), (4,5,6)


After a few tuples, MySQL may switch to a full table scan and lock the entire table for the duration. It should perform as expected once `FORCE INDEX (PRIMARY)` is added.  


You can read further information on 'FORCE INDEX' in the MySQL documentation here.