I've noticed that the approximation for abv ends up about 3 gravity points low for me.
In the spreadsheet? Low relative to what? It uses an approximation based on real extract, so it will be lower than (OG-FG)*131, but also more accurate.
Have you investigated how accurate your refrac is against a hydrometer on sugar water?
Yes, I calibrate using both water and a 20% sucrose solution. My hydrometer is two points low for both ("paper slip", presumably) but the refractometer is dead on at 0.0 and 20.0. In your case, are you sure it's the refractometer that's off, and not the hydrometer?