I agree that your DS may be a stealth dyslexic but I would be wary of the "vision based dyslexia" label. As Mich mentioned above, VT alone will not help. My DD finished her VT in the fall and so far the benefits are holding. Her tracking and focusing ability have improved and the headaches are gone.
VT hasn't changed how her brain functions. If you haven't, you may want to check out the Sally Shaywitz book "Overcoming Dyslexia." It has fMRI results showing differences in the way the dyslexic brain functions. When DD is well rested and emotionally happy, she compensates so well that it is easy to think that the problem is not that bad. When she is upset, tired or sick, it all comes out. I can even tell when she is getting sick by the subtle changes in her out loud reading.
I think that it is time for you to request a full evaluation from the school in writing. Even then, they may miss it. You may want to consider an evaluation by the Eides if you can afford it.
