Using 10.3, whenever I use zonal statistics, only about 90-95% of the records actually show up in the results. The remainders are blank though, if I navigate to that polygon, there is data present.
I've tried doing this in and out of geodatabase environments, with different shapefiles and rasters as my inputs, and still the same thing. It just seems to 'max out' in some way and not return all of the records. Often, the number of records returned on the same calculation is different. The same things happens if I use the Spatial Analyst 2 toolset, or an independent toolset I downloaded meant to calculate zonal statistics for overlapping polygons.
Anyone have any ideas?