I'm not sure why your sts are spiraling, a pic would be helpful. As for the toe, it sounds like you didn't have your sts in the proper place for kitchener st...did u kitchener the toe yet, is this what you mean, that when you grafted them together that they were up & down, rather than sideways? If this is the case, you had the sts misaligned; they should be on 2 needles, with one needle that has the sts from the instep (top of the sock/foot) and the other need that has the sts from the botton of the sock/foot after you have decreased & are ready to kitchener, this will allow for horizontal kitchener stitching. Now, if this isn't the case, I'm sorry, I didn't understand, but I'm sure someone else will.
OH, I just thought of this, with your spiraling rows, is this while you are decreasing the toes? If so, perhaps you chose a star toe on the sockulator? U can see a star toe here, but it usually doesn't require kitchener; but if you were decreasing in the same fashion, that could be your answer.
I'm terribly sorry that I couldn't be of more help.