Showdown not counting runs?

[RedJeff83_PSN]

I just had something weird happen. I have struggled with this 3rd inning showdown. So this is pretty frustrating. To make it clear.....I'm not complaining. Just asking if anyone else has had this happen.
I was at Sutter. He walks my lead off so bases loaded. Victorino hits warning track shot, and I tag up. Run scores and 2nd advances to 3rd. I then look at the score, and no run counted. Also have lost 2 outs. I figure I tagged early.
I am down 1 run, and am down to 3 outs. Same situation Victorino up, bases loaded. This time he hits a double. 2 runs score, and only 1 of them is counted.
I ultimately fail the challenge because the rest of my team sucks.....lol
Anyone else ran into this?