Histogram transforms are applied following this order: Red, Green, Blue and later the RGB composite (same adjustments to all channels). So, if you have changed the black or white points (shadows or highlights clipping) the RGB composite channel will not show the raw histogram, but the predicted one after all the prior adjustments. I think that this is issue that is happening to you. So far, none of our tests have found that the applied changes were different from what the user specified. As Larry said, try reseting the HistogramTransform instance after applying it, so you'll see the true raw data displayed at the RGB channel.