PHP OCI8 has two kinds of connection: non persistent and persistent. The persistent kind are designed to be held open. Is there some kind of timeout kicking in that is closing the connections?

Your version of PHP OCI8 is fine. There were some changes in OCI8 1.3 that can help connection management, e.g. better handling of bounced DB servers or dropped network links. Unfortunately until the PHP community replaces the pecl4win site, there isn't a PHP 5.2 build available on Windows - though you could compile it yourself.