[greymule]

It's a strange rule, and fairly recent.

R1 on 3B, R2 on 2B, R3 on 1B, two out. B4 gets a hit off the fence. R1 scores, R2 scores. B4 misses 1B but keeps running. R3 is thrown out at home for the third out as B4 stops at 3B.

The defense cannot appeal B4's (fourth out) miss of 1B, since B4 didn't score. However, had the defense not put R3 out, they could then have appealed B4 (for the third out) and nullified any previous runs.

Similarly, if B4 didn't even run but stood near the plate watching R1 and R2 score and then R3 get put out at home, the defense could not throw to 1B for the out on B4 to nullify the first 2 runs.