This is an old thread, but I thought I would post this link, as it helped me quite a bit on this issue. Essentially what it's saying is the server configuration can override the php config. From the article:
For example mod_fastcgi has an option called "-idle-timeout" which controls the idle time of the script. So if the script does not output anything to the fastcgi handler for that many seconds then fastcgi would terminate it. The setup is somewhat like this:
Apache <-> mod_fastcgi <-> php processes
The article has other examples and further explanation. Hope this helps somebody else.