This article is a good discussion on feeding chickens. Maybe since it is an Oregon State article it will carry more weight that what I say or a guy at the feed store says.
Oregon State Feeding Chickens
http://extension.oregonstate.edu/catalog/html/pnw/pnw477/#anchor1132074
A main difference in the feeds for different ages is the protein content. The starter, grower, and layer all have different formulations based on what is most efficient for the chickens at that stage of their development. Another difference in layer is that the layer mix has enhanced calcium, needed for egg shell production. Excess calcium can (not absolutely definitely that it will, but it can) damage internal organs on growing chicks. It may shorten their life expectancy or decrease thier laying efficiency. It would be long term damage so you probably will never know.
Feeding layer instead of starter and grower may delay egg production since they did not get the nutrients in the levels of their development that would have been most efficient. Not that it will, but it may. And the hens may lay less frequently, again because they did not develop most efficiently. In a small flock, you probably won't notice the difference. In a commercial operation with over 10,000 hens in one house, a small change in the laying rate can be significant.
I don't know what your vaccinations were for. Probably Marek's, possibly fowl pox, or maybe something else. The "medication" in medicated feed is not an antibiotic if it is called Amprol, Amprolium, or some derivative of this product. This is the active ingredient in most medicated feed. It does not cancel out any vaccinations. It limits the reproduction in the digestive system of the chicken of the protazoa that cause cocci. It does not kill the protazoa, it merely limits the number through reduced reproduction. It achieves this by blocking a vitamin the protazoa needs for reproduction. I don't know where Amprol falls in relation to "organic". With all due respect to those who are trying to go organic, and I do respect your personal choice, I personally don't care so I have never bothered to learn. I'm confident others on this forum will be able to respond to that if they see this thread.