Did it do this before the overhaul?
But just saying, hopefully without offense, if we accept your opinion that "all pictures are underexposed", then there would seem to be a problem, it ought not do that. But that is not in my experience, and my guess is that seeing it might be helpful too.
Not sure what it might show or help, but without a picture, no one can have any clue what we're discussing. And I'm not sure any one picture would be indicative of a general problem, so maybe 2 or 3 in different settings? (looking for the trend you suggest). With some details about settings and modes of course. If all pictures do this, then it should be easy to snap off about three of them, not of anything, the dog, the front door, a flower, the tree in the front yard, the lawnmower, just a picture, anything, not of anything, just some different situations showing typical exposures.
I don't have a D3100, but suspect it is like all other models. My guess is still that the issue must be more about generalities of proper exposure, which is always pretty hard to define critically. Everything always varies. Reflective meters are influenced by scene colors of course. Matrix metering going out of its way to look for unusual spots of high contrast, we never know what it does. Camera settings of Contrast and White Balance are large data shifts which affect extremes, even in Raw software...
In the raw editor, it would be instructive to pick any typical full range image, and run the White Balance slider from one end to the other while watching the histogram. At Tungsten end, blue is boosted substantially, and can clip. At Cloudy end, red is boosted substantially and can clip. Just how it is, all things vary.
You have not mentioned clipping though, seemingly more concerned about the black end, but blacks hopefully ought to be black (left end of histogram). But we really don't know what we are discussing other than an "all images" general case, but I doubt the the rest of us can comprehend that. 
Try to show us?
But just saying, hopefully without offense, if we accept your opinion that "all pictures are underexposed", then there would seem to be a problem, it ought not do that. But that is not in my experience, and my guess is that seeing it might be helpful too.
I don't have a D3100, but suspect it is like all other models. My guess is still that the issue must be more about generalities of proper exposure, which is always pretty hard to define critically. Everything always varies. Reflective meters are influenced by scene colors of course. Matrix metering going out of its way to look for unusual spots of high contrast, we never know what it does. Camera settings of Contrast and White Balance are large data shifts which affect extremes, even in Raw software...
In the raw editor, it would be instructive to pick any typical full range image, and run the White Balance slider from one end to the other while watching the histogram. At Tungsten end, blue is boosted substantially, and can clip. At Cloudy end, red is boosted substantially and can clip. Just how it is, all things vary.
Try to show us?
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