Good guess! Yes, if I do the pause before logging out, it is safe to log back in. And it is also safe to immediately re-enable logging as soon as I can (manually) do it.
So it might be as simple as enforcing a X second pause after addons have finished loading before data collecting can begin?
One of Blizzard's APIs must be in an unstable state as the game is first starting up, but then stabilize shortly afterwards?
btw, I'm not sure if zoning (as opposed to initial game log in) can trigger this bug or not, I'd need to find a place where you zoned into in area that was phased.