I think I was logging into my screens with the wrong account names and this was causing problems. But at the time I thought it was an issue with the key maps.
I've changed to a window layout that is better for me to keep track of which screen belongs to which account.
Note that you can look in ISBoxer and find the individual characters' virtual config files and go look at those manually to confirm what it's using for the login usernames. In WoW, it's in your WTF folder. In Rift, it's under %appdata%\Rift\...
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