When I bought an LED TV a couple years back the type of lighting the TV used was a major selling point. The issue you're having sounds like a result of the edge-lighting mechanism.
My understanding is that, as opposed to back-lit TVs, edge lit TVs illuminate whole sides of the television at a time meaning you get a reduction in lighting fidelity when there are only a few illuminated pixels against a dark/black background. I imagine small irregularities could exacerbate the problem, which results in the blotches you're seeing.
A few years back Samsung televisions were notorious for their lack of quality control so depending on how serious the issue is it may be worth returning.
http://www.avsforum.com/f/ is a tremendous resource. GL