Well, when I use it with MySQL, it is fine, but when I use it with MS SQL (the same queries), it gives me the timeout. I get the error (the timeout message) ussually with lines 222 and 500 of PEAR.php. And the query is not very big at all.
I'm working through the code as I type this message; I think it has more to do with the way that the PEAR database abstraction class returns DB_Result classes with the fetchRow() method.
--Jason