Aaron, it would have been more useful to CC Trevor, who is the author of that changeset. I've added him now.
I'm able to reproduce this with the mode-line as well, so it appears that there may be a bug there too in the code that was copied to implement the active/inactive faces in the header line. It's entirely possible that there's a bug in nano-modeline, but it seems suspect that code was added to consider windows and now this issue triggers when new windows are created (and possibly when selection changes, I haven't eliminated whether or not that's a factor yet).
You were able to reproduce what? I don't think you posted a recipe to reproduce the problem. Please do, if at all possible, preferably starting from "emacs -Q".