Assuming that you are using the latest versions (i.e. not an issue with OID/OBJECTID), and that you input stream is not a shapefile, there is a potential bug when the input dem is stored in a file geodatabase. Current workaround is to store the input dem on the disk. When the dem is in a gdb, some of the intermediate data is being cleaned up too soon. We will look into it.
Christine Dartiguenave
Esri Water Resources Team