1. When you call the Startup method you pass a FiddlerCoreStartupFlags as an argument (most probably the FiddlerCoreStartupFlags.Default value). In order to stop FiddlerCore of setting itself as proxy for the machine you should not pass the FiddlerCoreStartupFlags.RegisterAsSystemProxy value.
2. This guy seems to have found a solution and wrote it in a blog post
. You can give it a try.
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