Sounds like you need to host your WCF service in a Windows Service instead of IIS 7. Here is a blurb on the reasons to use a Windows Service for hosting WCF:
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Often, WCF developers must decide whether to host their WCF application inside of a Windows service application or inside of the Internet Information Services (IIS) or Windows Process Activation Service (WAS) hosting environment. You should consider using Windows service applications under the following conditions:
**Your application requires explicit activation. For example, you should use Windows services when your application must start automatically when the server starts instead of being dynamically started in response to the first incoming message.
**The process that hosts your application must remain running once started. Once started, a Windows service process remains running unless explicitly shut down by a server administrator using the service control manager. Applications hosted in IIS or WAS may be started and stopped dynamically to make optimal use of system resources. Applications that require explicit control over the lifetime of their hosting process should use Windows services instead of IIS or WAS.
**Your WCF service must run on Windows Server 2003 and use transports other than HTTP. On Windows Server 2003, the IIS 6.0 hosting environment is restricted to HTTP communication only. Windows service applications are not subject to this restriction and can use any transport WCF supports, including net.tcp, net.pipe, and net.msmq.
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Check out this link for more info: http://msdn.microsoft.com/en-us/library/ms734781.aspx