i mean, if its such a good pesticide- why dont they market it as such?
neem is used as an insect repellent (among other things) which is not the same as a pesticide - i.e. something that is toxic to insects. http://en.wikipedia.org/wiki/Neem_oil.

getting back to the thrips, they have now established a life cycle on your plants - they hatch, they grow, they mate and they lay eggs - which means you may be a bit late for a repellent to be effective.

If you still find thrips two weeks after the neem treatment you will need get something that will affect the thrips' metabolism and cause their death and so break their life cycle. nicotine works well as it intefers with insects digestion and respiration - they usually die within a few hours of exposure.