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.