Aha. The problem goes away after I SAVE THE CORRECTION, then the desynchronization gets fixed.

It's only desynchronized while I stay in edit mode immediately after making the correction.

Edit: also works to hit "reformat lyric".

The problem, as it was explained to me, is that changing the number of lines in the song isn't reflected in the time-cursor-position-gird until after the reformat command is done (which happens automatically after a save).