The difference is that FiddlerCore reverts your Internet proxy settings on exit.
Let me explain.
On startup FiddlerCore reads your Internet proxy settings and starts to use them as it own proxy settings. Then FiddlerCore changes your Internet proxy settings to 127.0.0.1:8888 (where FiddlerCore proxy runs). This is how FiddlerCore chains to the proxy you use.
On shutdown FiddlerCore changes your Internet proxy settings to the initial value.
Of course, this whole process is open for modification. I have just described the default behavior.
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