Putting the ND filter last, or closest to the lens, will cut down on reflections which result in lens flare.
Where-ever there is a surface in front of the lens (such as a filter), there is the potential for any small unwanted reflections bouncing from the lens to be reflected back into the lens and form lens flare. Here is an example of the type of lens flare you get from a UV filter. And this filter has an anti-reflective coating (from the green tinge, you may recognise it as a single-coated filter).
All glass surfaces will cause this, including the elements in the lens itself, but the elements inside the lens typically have very good anti-reflective coatings. You will get lens flare from the lens itself if there are strong light points in the picture, but you'll get more, and in some cases much more noticeable ones, if you have a filter in front of the lens.
An ND filter, especially one that's 3 stops or more, naturally reduces reflections simply because it reduces all light. Any reflections that pass through the ND filter will be reduced by 3 stops on the way out of the filter, then if there are further reflections from the outer surface of the ND filter or from subsequent filters, these will again be reduced by a further 3 stops as they travel back inwards. This reduces reflections by 64 times, for those reflections which pass through the ND filter twice.
If you have other filters between the ND filter and the lens, there is potential for reflections from the lens to bounce off these filters and back into the lens immediately without passing through the ND filter.
(This is the same reason why a lot of ND filters with 3 stops or more (8x or more) attenuation are not coated; they don't need it so much as the light attenuation of the filter itself is as good at reducing reflections.)
So to summarise, in so far as you get lens flare by having multiple filters, you'll get less lens flare by having the ND filter the closest one to the lens.