Did you try removing your ./sage/ directory? Especially your ./sage/init.sage file might be causing trouble if nonempty. (Of course, removing this would remove your notebook! But you could at least try renaming .sage/ to .sage-old/ temporarily; Sage would then create a new one and perhaps the problem would go away, and then you could do further debugging.)
Did you try removing your ./sage/.sage/ directory? Especially your ./sage/init.sage file might be causing trouble if nonempty. (Of course, removing this would remove your notebook! But you could at least try renaming .sage/ to .sage-old/ temporarily; Sage would then create a new one and perhaps the problem would go away, and then you could do further debugging.)