Could be due to processing or compression too.
Are you running through an AVR/prepro or other video device that may be doing some video conversion?
Though not the fault of the TV, I notice the blotchy black or smeared blacks on highly compressed feeds from the source (Direct TV, Comcast, Dish, etc..). When they push the video to your system they often compress it and something gets lost during the process. In the early days of HDTV, this was very common to see on any set. Also, sometimes I think analog signals get manipulated a lot and this can be the result.
Are you seeing it on all sources (TV, Bluray, etc..)?
Very good point. And besides the sources that you mention, low bitrate streaming (Netflix, Vudu etc) could also cause it. So yeah, it might not be a settings issue at all.