Make sure the geoprocessing extents include your whole project area. It seems the software will reset them to a wrong limit w/o me knowing about it and then I get confusing results. You can reset them under Geoprocessing>Environments. I use the DEM limits when I reset them.
It could also be a projection issue with your data so make sure the projections are all the same.
Last idea is that the process bombs for some reason and only processes part of the data. You'd think you would get an error message if this happened. A guess would be that the raster has some "null" value and the tool can't handle. In that case you could use the CON() function to make sure that there are not grids in the DEM that are null. This is a wild guess.
Please post the solution if you find one!