Renaming the CustomRules.js causes the SSL protocols to be remembered correctly, which is great. I don't understand how or why that should affect the setting, because the only thing I changed in my CustomRules.js was to uncomment the OnPeekAtRequestHeaders method, in which I added filters to hide some URIs I don't ever want to see. I literally copy-pasted that method into Fiddler from my old CustomRules.js, saved it, and everything (including the SSL protocols) just worked. So... weird. The only other thing I can think of is that I'm using the BCCertMaker.BCCertMaker instead of Fiddler's built-in one.
However the CONNECT issue persists, as you can see from this screenshot: http://imgur.com/VSgMPCK This occurs with 18.104.22.168 regardless of whether I'm using my old/broken CustomRules.js, a clean one, or my new modified one.
Bug reports aside, I'd just like to express my gratitude for your creation, and continuing support, of Fiddler. It's one of those tools that you honestly can't imagine living without once you've used it, and I'm certain it's saved billions of hours and millions of dollars in time for developers around the world. - yet this wonderful application remains free for anyone to use. Thank you Eric, and thank you Telerik, for being awesome.