Global Nav update shows subsites on PWA homepage?

From PWA level Site Settings->Navigation whenever adding a link to the Global Navigation section, the subsites start to appear on the PWA homepage.

This seems to happen regardless of the "Show subsites" checkbox.

Also, once the subsites show up, it doesn't seem to be possible to remove them.  We've tried to check/uncheck the "Show subsites" box, but it doesn't seem to apply to the root PWA home page. (<pwaurl>/default.aspx).

Is this a known issue?  Or is there a workaround?  Any other pages on the root site don't seem to have this issue (they obey the Show subsites setting).

Thanks,
Ryan