Query runs a long time in some newer MySQL versions
Just off the bat, newer versions of MySQL actually improve innodb performance (especially 5.5). I would highly recommend updating to this version if you're going to run InnoDB.
One method you could use to hunt down why it's taking so much longer is using MySQL Profiles
mysql> SET PROFILING=1;
mysql> SHOW TABLES;
mysql> SELECT * FROM foo;
mysql> SET PROFILING=0;
Query OK, 0 rows affected (0.00 sec)
mysql> SHOW PROFILES;
+----------+------------+-------------------+
| Query_ID | Duration | Query |
+----------+------------+-------------------+
| 1 | 0.09270400 | SHOW TABLES |
| 2 | 0.00026400 | SELECT * FROM foo |
+----------+------------+-------------------+
2 rows in set (0.05 sec)
mysql> SHOW PROFILE FOR QUERY 2;
+----------------------+----------+
| Status | Duration |
+----------------------+----------+
| starting | 0.000053 |
| checking permissions | 0.000009 |
| Opening tables | 0.000032 |
| System lock | 0.000010 |
| init | 0.000028 |
| optimizing | 0.000003 |
| statistics | 0.000012 |
| preparing | 0.000008 |
| executing | 0.000003 |
| Sending data | 0.000068 |
| end | 0.000004 |
| query end | 0.000007 |
| closing tables | 0.000008 |
| freeing items | 0.000013 |
| logging slow query | 0.000003 |
| cleaning up | 0.000003 |
+----------------------+----------+
16 rows in set (0.04 sec)
This should give you an indication of where it's hanging. From your explain output, you should try to get some indexing on the second and third tables instead of doing full table scans. But without DDL or the actual join columns, I can't suggest anything better than to research indexing strategies.
Using MySQL 5.5 out-of-the-box without proper configuration is like getting a Lamborghini and expecting topnotch performance on a gallon of regular gasoline (87 Octane).
You should expect better performance with high octane gasoline in a Lamborghini.
As with any database product, it is only as performance-enhanced as you actually configure it. Just like Spiderman said (8:36 - 8:40) : "WITH GREAT POWER, THERE MUST ALSO ALWAYS BE GREAT RESPONSIBILITY".
To get better performance out of MySQL 5.5, you must honestly configure certain things.
OPTION 1 : Use separate tablespace files for InnoDB, separating data and index pages from ibdata1
OPTION 2 : Configure options that engage more CPUs
OPTION 3 : Increase the number of threads dedicated for reads and writes
OPTION 4 : Properly tune InnoDB Options
OPTION 5 : Size your InnoDB Buffer Pool so it is large enough to hold all data, or 75% of installed RAM, whichever is smaller.
OPTION 6 : Use O_DIRECT for InnoDB Flushing
OPTION 7 : Use a dedicated DB Server, apart from LAMP, WAMP, XAMPP, Munin, and software like these.