Check your alignment while on the machine, I actually stressed out my knee on an elliptical and had had the same toe numbing problem before it happened. Make sure to be mindful of leaning more to one side or the other. Keeping your core strong will help also, it is not normal for you to feel numbness in your toes.
Happens to me too whatever footwear I use. ..I just ignore it now as the cardio is seriously needed! ! Sorry no help but at least you know you're not alone ;)
I have the same problem on the elliptical machine. My toes goes numb but I only get it on my right foot.
http://www.livestrong.com/article/297072-my-feet-go-numb-on-the-elliptical-trainer/