I know it is an old thread, but maybe someone find it useful. I had a similar problem in 1D steady and unsteady flow modules (both use same preprocesor for generating edges lines).
The problem was caused byinconsistent XS Cut lines – unsorted in my case. I was able to fix it manually (small case study) editing these lines in Geometry Editor\GIS Tools\XS Cut Lines Table. Removing the georeference from the cross sections did not work (HEC-RAS ver. 5.0.5).