Good luck eliminating all warnings. You should be able to minimize them by tweaking your headwater settings for time step under the outlet structure editor. Typically reducing the time step will produce more accurate results but will take longer calculating. Are you running ICPM? There are also some time step settings for this as well as convergence tolerances and max. iterations that can be found when you hit the GO tab and go from the default tab copmutations settings to the ICPM tab. Typically most errors of this nature are produced due to settings such as these but I doubt if you can remove them all.