Without your GIS shapefiles uploaded, I am guessing what could be the case. However, I suspect it is because you are using a newer version of ArcGIS or ArcMap. The recent release of these ESRI products (version 9.0 and newer) create 3D shapefiles, and not 2D shapefiles as prior versions of ArcGIS and ArcMap created.
The next release of StormNET handles 3D shapefiles.
However, in the interim, you can follow this procedure to "flatten" the 3D shapefiles to 2D shapefiles:
Technical Articles - ESRI Support