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I've had this happen a few times and I can't quite nail down why it does, but it makes me feel like I'm doing something wrong in the app. I mean, I'm scoring it right, but I'm not sure if I'm entering it right in the app. Here's the latest scenario.

Runner on first. Batter hits to 4 who throws to 6. 6 TAGS the runner for the out, and the hitter makes it to 1st on a FC.

I enter: IN PLAY > Fielder's Choice > choose 6-4. It asks me what happens to the runner who was on 1st and I choose TAGGED OUT. Here is where it asks me AGAIN for the defensive players involved in the play. Is that right? Why does it ask again? Doesn't seem to do that if Force Out is chosen, but I chose Tagged Out since that is technically what happened.

If I had to guess, it is that I should've used Force Out and only use Tagged Out when it is not a force play; NOT just because the runner was tagged. The runner was technically FORCED to run, it just so happen he was tagged instead of the SS stepping on the bag.

Your assumption is correct... on force plays we know the sequence is the same as what you entered for the batter initially, and you should always use it on a force play (even if the runner is technicaly tagged) because the force is designating the fact that the runner is being forced to leave their previous base.

Tag outs ask for touches again because a lot could happen for a tag out even if the batter was out on a standard 6-4, so we want to be able to capture that.

So just to be sure.... Runner was on third, batter hit to 2nd baseman. Fielders choice 4-2 occurred for an out at home. It is correct to have to enter 4-2 once for the FC and again for the tag out?

Yes, that is correct.