Arik,
Thank you for posting the files; they were very helpful in diagnosing the issue. Here are my notes:
1) The reason you are not seeing any forecast points output in the frxst_out csv file is that none of your forecast points are on a channel pixel (value = 0 in CHANNELGRID variable). You will need to move your forecast point by altering the latitude and longitude of the forecast points in your forecast point CSV file that is provided to the GIS Pre-processor. This process is described in the GIS Pre-processing documentation, Section 9.1 "Manual Specification of Station Points".
2), It looks as though you may have used a high-resolution DEM that had vertical units of cm. See the WRF-Hydro GIS Pre-processing documentation section 5.4.6 "Input Elevation Raster" for more information. You will need to convert this to units of meters. The GIS Pre-processing tools assume the vertical units of your input raster are meters, and because you provided a raster with units of cm the "Fill" process reached the maximum fill limit (default of 1000m) in many locations. The resulting channel network is then highly discontinuous. If you use a DEM with vertical units of meters, you will see a continuous channel network without breaks in the network.
I think following this guidance will help to resolve the original issue you inquired about and provide a more realistic simulation.
Kevin