The case of the mysterious MySQL caching across restarts

I found a very slow MySQL query in my web app. The weird thing is that the query is only slow the first time it's executed, despite the fact that the query_cache is set to its default (query_cache_size 0) like so:

mysql> show variables like 'query%';
+------------------------------+---------+
| Variable_name                | Value   |
+------------------------------+---------+
| query_alloc_block_size       | 8192    |
| query_cache_limit            | 1048576 |
| query_cache_min_res_unit     | 4096    |
| query_cache_size             | 0       |
| query_cache_type             | ON      |
| query_cache_wlock_invalidate | OFF     |
| query_prealloc_size          | 8192    |
+------------------------------+---------+

The even weirder thing is that this speedup persists even after the MySQL server has been stopped and restarted (I'm using OSX, and perform this restart using the system preferences pane.) The only way I can re-create the poor performance of the initial query is by rebooting the system.

So my question is: how is this happening? Obviously some sort of caching at work, but where? And how does it persist across database restarts? This query is mediated through our web app, which comes via PHP/Apache, but there are no extra bells and whistles, and the curiou开发者_如何学JAVAs caching also persists across Apache restarts.

Help?

wild guess is operating system, or hard disk, caching the file