It can't possibly be a skin disease ( or nutritional problems) of any kind because it's location is so specific to the knuckle of the large toes. It is just not possible for any disease to target only the knuckle of both large toes !
If it were any kind of skin disease, then it would show up in areas in addition the large toe knuckles.
How old were you when this condition first appeared? How many years has it been going on?
Does anyone in your family have a similar condition? I am thinking it is caused by DNA and you inherited the condition.