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 <field names>
FROM <table1>
INNER JOIN <table2> ON <join_condition>
INNER JOIN <table3> ON <join_condition>
INNER JOIN <table4> ON <join_condition>
...
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.