Changes in vegetation over the month between your scenes could be part of the issue. It is also possible that there is some haze over areas of your scene outside of your dark object location(s), and therefore this haze is not being removed during your atmospheric correction.
Another reason that you see contrast between the two scenes could be due to inconsistent dark-object subtractions (DOS) made during your atmospheric correction. This is very likely to be the case if you are using the darkest pixel in each scene rather than the same location. The reason is that the darkest pixel in one scene might be a shadow from a cloud over a forested area, while the darkest pixel in the second scene might be a cloud shadow over bare soil. This difference, even though the values are small, will be very apparent when you try perform your fill. In fact, you might find that there is less contrast when you simply fill with NDVI calculated from reflectance - without any atmospheric correction.
If possible, you might try a different method for your atmospheric correction such as FLAASH. If for some reason you can't use a different method of atmospheric correction, try to select the same dark-object location in both scenes (though this might be a problem because you won't have a lot of overlap between two Landsat 7 scenes).
Hope that helps.