Hm, SpriteFont object behavior is kind of erratic with Anchor behavior enabled. Could be because SpriteFont works out its own positioning and scaling for each glyph. I'm not sure how Anchor works, but it tries to force reposition or rescale the object, which can cause unforeseen consequences.
However I didn't encounter any disappearances, just jarring and wonkiness. Eh, all the same.
Guess I'll need to rewrite SpriteFont in the future, to better work with new exporters. I'll change the way it works positioning and scaling out then.