Yes, this a long-standing bug and I don’t have a good solution for it. I tried several times to mitigate this issue and failed.
Please note that Folders on Top feature had to be reimplemented for pretty much every major OS release. I believe that this problem is not present in earlier OS releases and is also not an issue in Sierra (the feature was replaced by Apple’s implementation of “folders on first”).
I’m sorry for the inconvenience.
sorry, i tried to look for any previous duplicate reports of this issue, couldn’t find any.
btw a handy workaround for those who like quick keystrokes is just something like
i.e. if you default to view by list, like i usually do, then you can just quickly sort-resort the view (view it as something else then view it back as it was first time) as a reflex keystroke action, and then the new folder appears correctly.