Have you try using different rendering mode in the official release of HECRAS5?
Right click on Result in RasMapper and try it out. That might solve it.
It is fantastic with better RAS mapper capabilities. The SI version for linking internal boundary has been fixed. I am testing the precipitation option and it is possible to extract the total flow across the internal boundary.
download and follow through the menu. You need some engineering background on hydraulic and one dimensional analysis to understand the mechanism in HECRAS
1mx1m cell size, time step of 30 second using full momentum. Sure you could post it. I have posted a version of normal crossing and a version with downstream tidal effect.