I finally got it to work...kinda.
So I followed your instructions, like you said. I uninstalled all of Reaper. Reinstalled it into my original user account and lo and behold all of my preferences were there. So then I exported my preferences. I then went to my new user account which I've been trying to migrate to and it had the same problem. It refused to look in the Application Support folder where it should and instead just decided to put all of those files in whatever directory I first opened Reaper in. For example if I dragged Reaper from the dmg to the desktop then when i opened Reaper it would create all of those configuration files in the desktop. So finally I decided to first move reaper to a new folder inside of Applications called Reaper. It still did that same annoying thing but at least it was contained in one directory.
Next I imported the configurations from my other user account. (
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So I guess it's pretty much fixed. I've got all my preferences and whatnot. I just wish I could understand why it's behaving this way. I have a feeling that Reaper for some reason doesn't like that I'm using two different user accounts.
Also, if possible I would love it if when I use REaper in either user account that it would use the same preferences directory. That way if I changed a preference on one side then it would change on the other as well (though that feature isn't really a dealbreaker for me.)
One last thing (sorry for the long message) for some reason some of my VST's aren't working though I'm 90% sure that's an unrelated problem because they were missing before all of these problems happened.