If the Input raster or feature zone data (in_zone_data in Python) is a feature, for any of the zone features that do not overlap any cell centers of the value raster, those zones will not get converted to the internal zone raster. As a result, those zones will not be represented in the output.
To avoid this, ensure that each of your zones contains one or more cell centers. You can create more cell centers by specifying a smaller cell size in the environment. The default analysis cell size comes from the value raster. Therefore, specifying a Cell Size that is smaller than that of the value raster will enable more zones to be captured. Keep in mind that specifying a smaller cell size, will generate a larger output raster. Even more important, the higher resolution output may give the wrong perception of a higher quality result than what it actually is, since the additional detail does not actually exist in the input value raster.