I believe the buffered counting could be the problem. You might consider posting to the daq forum for help on this aspect of your code.
Were you able to learn anything when you auto indexed your wires? I was thinking over lunch that the default values for numerics is zero and when you concatenate arrays of different lengths the shorter one is increased in length with default values. If your loop itterats fewer times than you think, this would explain the column of zeros.
