I suspect that using "JOIN" is doing a "LEFT JOIN". Try using an "INNER JOIN" and see if the explain statement is the same.
SELECT
FROM
INNER JOIN ON
INNER JOIN ON
INNER JOIN ON
...
When using an inner join, I would not expect there to be a performance difference between your two queries. I would worry more about having the proper indexes. Make sure the join conditions can make a match using an indexed column.