Hi Kate,
I too have had similar problems. I don't know whether you've had proper advice yet, but if it is the ball of the great toe, that you are getting the pain from the small sesamoid bone which run in the split tendons of a small muscle (flexor hallucis brevis).
Fortunately, when I had this problem, rest, and softer cushioning have more or less resolved the problem for me. I imagine exercises for the intrinsic foot muscles, such as toe press-ups could help in the long run.
If you havenit yet, do see a podiatrist who can relieve the problem by customising footwear, or by simply putting felt around the area to prevet your weight being taken on the painful area.
Good luck,
Mowgli.