It would be very helpful if you could be much more specific about how many milliseconds you're seeing.
Creating a certificate takes time, potentially a few seconds, depending on the length of the RSA key. Fiddler and FiddlerCore offer three different root certificate generators:
MakeCert (provided by MakeCert.exe)
CertEnroll (used if MakeCert.exe isn't present, on Win7+ only)
BouncyCastle (provided by CertMaker.dll/BCMakeCert.dll)
Each of these takes a different amount of time, and those times are pretty much the same whether you're using Fiddler or FiddlerCore.
The issue that you're encountering is almost certainly the fact that Fiddler creates a root certificate *once*-- when you first enable decryption of HTTPS traffic, then reuses that root on subsequent runs. In contrast your FiddlerCore-based application might
end up doing this every time it runs.
When your app runs, what is the information output to the FiddlerApplication.OnNotification
event handler with regard to certificate generation?
If you're using BouncyCastle/CertMaker.dll, are you caching the root certificate and private key via a preference? See http://weblog.west-wind.com/posts/2014/Jul/29/Using-FiddlerCore-to-capture-HTTP-Requests-with-NET look for the text :
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