I believe this is still a bug that hasn't been fixed yet (at least the last I looked). See this thread...
http://forums.arcgis.com/threads/31888-Hydrology-Flow-Direction-tool-output-quot-incorrect-quot-when...
Wes
Hi Pavan,
Was this issue resolved? It appears I am having the same issue using ArcMap 10.5.1. Applying the maximum depth figure from the MINUS tool output as the z value in the Fill function only produces the same as running the Fill tool without it.
Thanks,
Ilan