As we don't use "proxifer" here, I don't think we can answer that question. It sounds like that tool has a bug; you may wish to contact their support team to get help.
If that tool offers a settings screen where an "upstream" gateway or proxy can be specified (e.g. the middle of this article: http://www.proxifier.com/new/ver3.htm), you should ensure that when Fiddler is not running that tool's settings indicate that traffic should be sent directly (no gateway) to the server.
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