What you're describing is that the client is required to present a ClientCertificate when authenticating to your website. When running Fiddler, Fiddler will not automatically challenge the client to provide a certificate and as a consequence the login will fail while Fiddler is running. Manual configuration of Fiddler is required to allow Fiddler to present a client certificate on the user's behalf; this process is described here: http://fiddlerbook.com/Fiddler/help/httpsclientcerts.asp
Now, it sounds like you might
be saying that users are having problems logging in even when Fiddler is not running
. That would not make very much sense, as the certificates that Fiddler uses do NOT contain the ClientAuthentication key usage flag and thus their presence should have absolutely no impact whatsoever on the client when Fiddler is not running.
Fiddler's certificates can be automatically cleaned up ever time Fiddler exits; see https://groups.google.com/forum/#!topic/httpfiddler/Yg4G7SWl3bo
thanks for the extra info,
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