I find that if I have two objects overlapping in Blender and export to STL, the object is terrible in Slic3r and Cura (though Cura is better).
Turn on wireframe mode and see if there are vertices and/or faces inside of the object (instead of just on the surface). These can cause portions of the surface to not be printed. I had a piece with two legs that come together at the bottom and the overlapping portion was “missing” when rendered in Cura (layers mode) or in Slic3r.
Use the 3D Printing Toolbox for Blender and it will help to find and, in some cases, remove these problem areas.