FMS XML (fx.php) Queries Stop Responding

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I have a client with an php web site developed in fx.php in FileMaker 11. We switched them to FMS 12 on IIS 7 and Windows 2008 server. For some reason the web pulishing engine stops responding to new requests after a certain amount of time. We tried using both native PHP 5.3 and the FIleMaker supplied one, but the problem is still happening. The only solution so far has been to reset the web publishing engine. Any one else having this problem?