Had this happen. I was the second base umpire in a 4 man system in little league. Runner on 1st with one out and the batter hits a basehit to the right center gap which was cut off and then a throw made to third base. As R1 rounded second base the runner made contact with the shortstop. I pointed and yelled thats obstruction. The runner made it to third base safely but rounded the base a little too far and then the runner got caught in a run down. As this was beginning to take place the batter/runner rounded 2nd base and you got hit made contact with the shirtstop, to which again I pointed and yelled thats obstruction. The rundown finished and the runner made it safely back to third. Now we had runners at second and third and in my judgement the runners ended up with the bases they would have acquired. The runner going into third was protected by me to third base and in my opinion the runner on second would not have advanced further then where the runner was. So in essence, I kept the runners at second and third as I thought they would not have gotten any further then those bases
With R1 rounding 2nd, heading for 3rd, I believe the throw to 3rd base was a play on R1.....and R1 being obstructed rounding 2nd was obstruction #1 resulting, by rule, in a immediate dead ball under Rule 7.06(a) With the ball dead there cannot be a 2nd obstruction call on the batter-runner.
Then umpire's judgment as to where both runners would of reached... under 7.06(a).... kicks in.
LOL! I was trying to answer this a few days ago when ACTIVE.COM crashed! [Happened again TODAY!]
R1 was obstructed near second base. That's Type B. Your ruling will be to protect R1 as far as you think he would have made it had there been no OBS. Sounds like you protected him to 3B ONLY!
Then when he overran 3B, he was vulnerable.
When he gets in a rundown, if there is OBS, it's Type A! In that case, you call time, site OBS, and award the runner one more base past the one he legally attained! He scores! BR stays at 2B.
Yes, you had two cases of OBS: one does NOT automatically kill the play, and you properly let play continue after he had reached the protected base (assuming no play yet.) The other requires immediate call of time and a one base award because a play is being made on the obstructed runner. A rundown is clearly a play being made, and even though someone without the ball does the OBS, he's part of that play!
A lot of coaches train their kids in a rundown to bolt immediately towards the fielder who just threw the ball to draw OBS. Other coaches teach that as soon as you throw the ball to the other fielder, GET OUT OF THE BASEPATH! That's why an alternate fielder should roll in behind.
You should have scored R1, IMO.