What it comes down to is the CLR host. The ASP.NET host is hardcoded to use the Web.config file as its configuration file. The executable loader by default uses yourapp.exe.config. In your case, it's odd that aspnet_wp.exe.config is being used. In any case, if you are using a wrapper, perhaps your wrapper has a chance to create the AppDomain that hosts the COM+ service itself? If so, when you are configuring the AppDomain, you can specify any .config file you want so long as the CLR can resolve the location. See AppDomain.SetupInformation for more details.
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