I would guess it would have something to do with the projection you are using, and whether you used a planar or Geodesic Buffer when you used the Buffer tool. If you are working with a geographic coordinate systems instead of a projected coordinate system, it does not take into account the curvature of the earth when calculating distances with the select by location(within a distance).
http://gis.stackexchange.com/questions/131766/why-the-select-by-location-analysis-calculates-distance-in-a-wrong-way
Good deal. Thank you.
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