[tibear]

I've found my answer and learned something in the process. Further explanation for 4.09 gives:
Approved Ruling: No run shall score during a play in which the third out is made by the batter runner before he touches first base. Example: One out, Jones on second, Smith on first. The batter, Brown, hits safely. Jones scores. Smith is out on the throw to the plate. Two outs. But Brown missed first base. The ball is thrown to first, an appeal is made, and Brown is out. Three outs. Since Jones crossed the plate during a play in which the third out was made by the batter runner before he touched first base, Jones' run does not count.

Learn something new everyday.