You could create your program as Windows Service (NT Service) so OS starts it up for you and takes care for it. I think Visual Studio (at least pro version) has template for services. Or you could google for something like C# .NET Windows Service.
This doesn't necesserily correct your situation but at least it would be more elegant solution than using scripts :) Oh, and in Vista I think there's some service level that could be used to start resource consuming services (it delays service startup until all the necessary stuff is loaded).
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