Am facing a similar issue but with a different process. The initial steps, i.e exporting data to HEC GeoRAS and then exporting it back to GIS, all went fine.
Could even create the water surface profiles also.But when I try to delineate flood plain , after a long runtime process of 45 mins it shows the following error, as in the depth profile is created but the the boundary profile is not created. Please refer the attachment and kindly help.