If you say the scale is fine, do you mean that the Scale is (1, 1, 1) as it should be, or that the Dimensions are fine?
Duplicating Objects instead of creating them won’t make Bevel problems (as far as I know). Although, without any screenshots or even a link to your .blend file, all we can do is guessing.
And you cannot change the default size of newly created objects, unless you dive into Blender’s source code and change it there (which you may, of course).
