I am attempting a spatial join in ArcMap using the spatial join tool to count identical overlapping polygons in the same feature class. I have run this analysis a number of times without problem. Since today, the Join_Count field is populated with zeros even though the analysis has been completed. It is clear the analysis has been done because the rows are ordered by the Shape_Length and Shape_Area fields, where none of the first rows have identical values in those fields (i.e. no overlaps), but successive rows do. When I use the Identify tool to select one of the rows which has the same values as successive rows, the number of identified features matches the number of rows with identical Shape_Length and Shape_Area fields.

I am using the same feature class (WGS 1984 UTM Zone 48N) as the target and join features in the spatial join analysis, so I don't believe the problem can relate to coordinate/projection issues as seems to have been the case for many of the other help requests related to null values in spatial join.

I am working on a dataset containing around 2 million polygons. Because analysis on the whole dataset is problematic from a memory perspective, I am running spatial join on feature classes clipped from the main dataset. The first clip worked fine. But the second and third have the zero Join_Count fields.

Can anyone shed any light on this for me?

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