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It may also be that the new indexes aren't being stored after chrome.tabs.onUpdated. That's the other problem that I was having. 

I surmise that the issue has something to do with not storing the tab reference of the new tab after it's created, and then using the original tab reference's index when doing the refresh. I ran into a similar problem with an extension that I was previously developing for work.

As of today (11/24/2015), my tabs are also still moving around on their own. Is it possible to just put in an option that prevents the app from changing the indexes on the tabs? I recognize the value in putting the tabs in the same order as they are in the hierarchy, especially when users like me have a zillion tabs open, but it can also be irritating when I'm trying to debug something, and the tabs keep changing order. Thanks!!!