The problem to be addressed here is understanding whether a run should score when 2 are out. There are three basic tenants to the run being legitimately scored or not scored to keep in mind, which are required for all umpires to understand.
First: No run can score when the third out is made by the kicker-runner not reaching first base safely. If a base runner on third crosses the plate with two out before the kicker-runner is put out on a ground out or a fly out, the run does not score. Similarly, with runners on first and third, if the runner on third scores before a conventional double play (i.e. 6-4-3) is completed, the run does not score.
A trickier example is bases loaded, 2 out. The kicker kicks a home run but fails to touch first base. After all runner have circled the bases, the ref calls the kicker out at the conclusion of the play. All runs are nullified (no runs score) since the kicker-runner is out at first and did not reach first safely.
Second: If the third out is recorded on a force play, no run can score. For example, runners on first and third, 2 out. A slow roller is kicked to the third baseman who charges and throws home, but the tag is not made before the runner crosses the plate. The runner from first had stumbled and fallen before touching second. The kicker-runner has reached first base. The catcher then throws to the second baseman who tags the runner for the 3rd out before he reaches second. Though this is a tag play, the runner from first is still forced to second, hence the run does not score.
Keep in mind that if a runner misses a base to which he is forced with 2 out and the ref calls them out at the conclusion of the play, no run can score regardless of any action that takes place after the missed base. Also, a force play occurs only when runners have to advance because the kicker becomes a runner.
Third: There can never be a force play when a fly ball is caught. Here is an example that is often called incorrectly. With runners on first and third with one out, the kicker kicks a fly ball to the outfield that is caught. The runner on third legally tags and scores, but the runner on first goes half-way and fails to tag. The outfielder throws to first and the throw beats the runner attempting to return to first. The run from third counts, since this is a time play and the run scored before the 3rd out was made at first. When the ball was caught in the outfield, the runner on first is not forced to second, but is free to return to the base. Since a tag at first is not required (the ball must only beat the runner to the bag and be in legal possession of a defensive player), many umpires incorrectly interpret this as a force play and do not score the run.
A time play is a play where if the runner crosses the plate before the 3rd out is made, the run scores. A common example is runner on second, 2 outs. The kicker kicks a ball in the gap but is thrown out at second. If the run crosses the plate prior to the 3rd out, it counts. The kicker-runner safely reached first and there is no force out.