VSP will be based on your Medical Pay Entry Base Date which is usually the day you are recommissioned as an O3. It is not the first day of active duty. If you have prior service, that does not count towards that time either.
This is true even if you have a deferment. So, if you are deferred for a General Surgery Residency that lasts 6 years, when you start payback you should get the $1K per month.