Yep, unfortunately chat windows are odd creatures.
As an additional example, if you have custom chat channels in the primary chat window (even if it's in different tabs in it) the main tab absorbs them. But they're perfectly fine if they're in a second window. Odd, no?
Deleting your uisettings file will reset the windows to their old locations, unfortunately.
As for the old windows reapparing, I'm convinced that it is because at one point that was the 0th (or 1st, depending how you count
) chat window and the game somehow remembers that and just doesn't want to let it go. But that's just a theory.
For the time being, I'd just add it as a tab and ignore it, that way it'll be less bothersome.