you are probably running the program after you got out of the end of game screen. to do it right: after you finish the game there's a boxscore and quit option (if you're using it for a dynasty). minimize your game and run the extractor. that will extract the boxscore with the right teams and everything. i know this because it just happened to me. i had forgotten to run it after the game ended and i went back to the dynasty main scrren, then i decided to extract the boxscore but i got the giants and another team even though it was Yankees vs. Twins.
hope this helps you solve your dilemma. (i think i spelled that right, lol)