An image of what you're trying to accomplish, or at least a more thorough description of the problem, would help.
That's a bit odd. Since the stringers appear to join properly on the other side, my guess would be that the stringer on the open side doesn't join because of some conflict resulting from the length of the topmost tread. It appears that the distance from the edge of the landing to the top nosing is less than 1 full tread depth, which might cause the stringer to not show up there. Try adjusting the landing to see if that fixes it. If so, there may be some other adjustments we can make to get it to work in the original configuration, but first we need to identify what's causing the problem.