Are you using at.js or mbox.js for your implementation? A4T only works with at.js 0.9.6 or later, not with mbox.js. Also, have you looked in Target to see what numbers it is reporting? I would check Target to see what it is reporting and see if its more accurate than A4T.
If Target is correct, then most likely this is only a reporting issue, not an issue splitting traffic. In other words, its quite possible that your test is running correctly and splitting traffic correctly, but its just reporting wrong through A4T.