Without knowing more (posting some of your code would help) it's difficult to say exactly what the problem is. I suggest that just before you load the new values for ‘xdata’ and ‘ydata’, you set your data arrays to the empty array:
xdata = [];
ydata = [];
Otherwise, be sure you're actually not loading your previous run data. If they're in a matrix, you could have a matrix indexing error, so the vector you believe you are loading is not the one you are actually loading.
