Using the stock end links on a lowered car is not a good idea. The end links should be the right length (i.e. not preloaded). Using stock links (if they are the wrong length) could result in this:
http://blogs.eurotuner.com/6467795/e...nks/index.html
Assuming the links are having nothing wrong with them (like torn bushings), any noise is the result of not tightening the adjustable links tight enough. I chased this problem with my adjustable end links for a while. I would tighten them (pretty tight I thought) and the noise would temporarily go away.
When I had the car in for other service, I told the mechanic about the noise. He tightened up the links and said that was the problem. I asked him how tight to make them and he said "tighten them to the point where you feel like they might break". I obviously did not tighten them that much. I suspect some other people here with the end link noise did not tighten them up enough either. Since he tightened them (a month ago - about 1k miles) the noise has not come back.