The ND source is slightly wider too, by about 0.1 pixels. Here's another way to look at it. There are at least two effects that lead to this, and it's not clear which is dominant. The first is that for shorter exposures, there are more negative pixels included in the total emission. Note that we're making a distinction between 'Dark Current' and 'Background'.
Background is what's left over, in the dimmest part of the image.
The different exposure levels are denoted by dark blue, light blue, green and orange stars as before. The shortest exposures have the lowest background level, and longer ones have higher levels. All of these images have had the same values of the dark current subtracted, a common happening before the entrance filter holes, so this is a reflection of the original data. This background is not due to scattered X-rays from the source, since it does not follow the flare time profile. The excess background could be X-rays from the active region behind the flare, or straylight.