I have statements like this that are timing out:
DELETE FROM [table] WHERE [COL] IN ( \'1\', \'2\', \'6\', \'12\', \'24\', \'7\', \'3\', \'5\')
If the table you are deleting from has BEFORE/AFTER DELETE triggers, something in there could be causing your delay.
Additionally, if you have foreign keys referencing that table, additional UPDATEs or DELETEs may be occurring.